| Bacteria | | Proteobacteria | citrus huanglongbing (greening) disease (citrus greening) | Present | | | Aubert et al., 1985 |
| Bacteria | | Proteobacteria | Liberibacter asiaticus (Asian greening) | Present | | | CABI/EPPO, 2006; EPPO, 2014 |
| Bacteria | | Proteobacteria | Xanthomonas oryzae pv. oryzicola (bacterial leaf streak of rice) | Present | | | EPPO, 2014; CABI/EPPO, 2015 |
| Eukaryota | Fungi | Ascomycota | Ceratocystis fimbriata (Ceratocystis blight) | Present | | | Tayler & Stephens, 1929 |
| Eukaryota | Fungi | Ascomycota | Fusarium oxysporum f.sp. cubense (Panama disease of banana) | Present | | | CABI/EPPO, 2015 |
| Eukaryota | Fungi | Ascomycota | Mycosphaerella fijiensis (black Sigatoka) | Present | Introduced | Yes | CABI/EPPO, 2011; EPPO, 2014; Carlier et al., 2000a |
| Eukaryota | Fungi | Basidiomycota | Phakopsora pachyrhizi (soyabean rust) | Present | | | CABI/EPPO, 2015 |
| Eukaryota | Fungi | Basidiomycota | Puccinia kuehnii (orange rust) | Present | | | EPPO, 2014; CABI/EPPO, 2015 |
| Eukaryota | Metazoa | Arthropoda | Aleurocanthus woglumi (citrus blackfly) | Present | | | EPPO, 2014; Mound & Halsey, 1978 |
| Eukaryota | Metazoa | Arthropoda | Anoplolepis gracilipes (yellow crazy ant) | Present | Introduced | Yes | ISSG, 2011 |
| Eukaryota | Metazoa | Arthropoda | Bactrocera carambolae (carambola fruit fly) | Present | | | |
| Eukaryota | Metazoa | Arthropoda | Bactrocera cucurbitae (melon fly) | Present | | Yes | Drew, 1982; CABI/EPPO, 2003; EPPO, 2014 |
| Eukaryota | Metazoa | Arthropoda | Bactrocera dorsalis (Oriental fruit fly) | Present | Native | | Drew & Hancock, 1994; EPPO, 2014 |
| Eukaryota | Metazoa | Arthropoda | Chrysomya bezziana (Old World screw-worm) | Present | Native | Yes | Wardhana et al., 2012b; Wardhana et al., 2014 |
| Eukaryota | Metazoa | Arthropoda | Conopomorpha cramerella (cocoa pod borer) | Widespread | | | CIE, 1984 |
| Eukaryota | Metazoa | Arthropoda | Diaphorina citri (Asian citrus psyllid) | Absent, unreliable record | | | EPPO, 2014 |
| Eukaryota | Metazoa | Arthropoda | Dysmicoccus brevipes (pineapple mealybug) | Present | | | CIE, 1972 |
| Eukaryota | Metazoa | Arthropoda | Erionota thrax (banana skipper) | Widespread | | | Maruyama, 1991 |
| Eukaryota | Metazoa | Arthropoda | Euwallacea destruens | Present | Native | | Wood & Bright, 1992 |
| Eukaryota | Metazoa | Arthropoda | Euwallacea fornicatus (tea shot-hole borer) | Present | | | EPPO, 2014 |
| Eukaryota | Metazoa | Arthropoda | Euwallacea piceus | Present | Native | | Wood & Bright, 1992 |
| Eukaryota | Metazoa | Arthropoda | Heliothrips haemorrhoidalis (black tea thrips) | Present | | | zur Strassen, 1994 |
| Eukaryota | Metazoa | Arthropoda | Nezara viridula (green stink bug) | Restricted distribution | | | Chu, 1979; CABI/EPPO, 1998 |
| Eukaryota | Metazoa | Arthropoda | Oryctes rhinoceros (coconut rhinoceros beetle) | Present | | | EPPO, 2014; CABI/EPPO, 1998 |
| Eukaryota | Metazoa | Arthropoda | Papilio demoleus (chequered swallowtail) | Present | | | Matsumoto, 2002 |
| Eukaryota | Metazoa | Arthropoda | Papilio demoleus (chequered swallowtail) | Present | | Yes | Matsumoto, 2002 |
| Eukaryota | Metazoa | Arthropoda | Phyllocnistis citrella (citrus leaf miner) | Present | | | Kalshoven & van der Laan, 1981; Waterhouse, 1993; CABI/EPPO, 2003; EPPO, 2014 |
| Eukaryota | Metazoa | Arthropoda | Plutella xylostella (diamondback moth) | Present | | | Sastrosiswojo & Sastrodihardjo, 1986 |
| Eukaryota | Metazoa | Arthropoda | Rhynchophorus ferrugineus (red palm weevil) | Present | | | CABI/EPPO, 2010; EPPO, 2014 |
| Eukaryota | Metazoa | Arthropoda | Scyphophorus acupunctatus (agave weevil) | Present | | | Vaurie, 1971; EPPO, 2014 |
| Eukaryota | Metazoa | Arthropoda | Sitobion miscanthi (indian grain aphid) | Present | Native | | Blackman & Eastop, 2000; CABI/EPPO, 2003 |
| Eukaryota | Metazoa | Arthropoda | Spodoptera exempta (black armyworm) | Present | | | EPPO, 2014 |
| Eukaryota | Metazoa | Arthropoda | Spodoptera litura (taro caterpillar) | Present | | | EPPO, 2014 |
| Eukaryota | Metazoa | Arthropoda | Xyleborus perforans (island pinhole borer) | Present | Native | | Wood & Bright, 1992 |
| Eukaryota | Metazoa | Arthropoda | Xyleborus similis | Present | Native | | Wood & Bright, 1992 |
| Eukaryota | Metazoa | Arthropoda | Xyleborus volvulus | Present | Introduced | Yes | Wood & Bright, 1992 |
| Eukaryota | Metazoa | Arthropoda | Xylosandrus ater | Present | Native | | Kalshoven, 1960; Wood & Bright, 1992 |
| Eukaryota | Metazoa | Arthropoda | Xylosandrus compactus (shot-hole borer) | Present | Native | | CABI/EPPO &, 1997; EPPO, 2013 |
| Eukaryota | Metazoa | Arthropoda | Xylosandrus crassiusculus (Asian ambrosia beetle) | Present | Native | | Wood & Bright, 1992; CABI/EPPO, 2009; EPPO, 2014 |
| Eukaryota | Metazoa | Arthropoda | Xylosandrus morigerus (brown twig beetle) | Present | Native | | Wood & Bright, 1992 |
| Eukaryota | Metazoa | Chordata | Bubalus bubalis (Asian water buffalo) | Present only in captivity/cultivation | | | Borghese, 2005 |
| Eukaryota | Metazoa | Chordata | Columba livia (pigeons) | Present | Introduced | | ISSG, 2011 |
| Eukaryota | Metazoa | Chordata | Rattus rattus (black rat) | Unconfirmed record | Introduced | Yes | ISSG, 2011 |
| Eukaryota | Metazoa | Chordata | Trachemys scripta elegans (red-eared slider) | Present | Introduced | | ISSG, 2011 |
| Eukaryota | Metazoa | Mollusca | Lissachatina fulica (giant African land snail) | Present | | | EPPO, 2013 |
| Eukaryota | Metazoa | Mollusca | Pomacea canaliculata (golden apple snail) | Present, few occurrences | Introduced | Yes | Hendarsih-Suharto, et al., 2006 |
| Eukaryota | Plantae | Pteridophyta | Salvinia molesta (Kariba weed) | Widespread | | Yes | Nguyen, 1976 |
| Eukaryota | Plantae | Spermatophyta | Acacia auriculiformis (northern black wattle) | Present | Introduced | | |
| Eukaryota | Plantae | Spermatophyta | Acacia crassicarpa (northern wattle) | Present | Introduced | | Turvey, 1996; Otsamo & Adjers, 1995 |
| Eukaryota | Plantae | Spermatophyta | Acacia mangium (brown salwood) | Present | | | |
| Eukaryota | Plantae | Spermatophyta | Acacia mearnsii (black wattle) | Present | Introduced | | CABI, 2005 |
| Eukaryota | Plantae | Spermatophyta | Albizia procera (white siris) | Present | Native | | Nielsen, 1985; Valkenburg, 1997 |
| Eukaryota | Plantae | Spermatophyta | Aleurites moluccanus (candlenut tree) | Present | Native | | Govaerts, 2014 |
| Eukaryota | Plantae | Spermatophyta | Alocasia macrorrhizos (giant taro) | Present | Native | | USDA-ARS, 2012 |
| Eukaryota | Plantae | Spermatophyta | Artocarpus altilis (breadfruit) | Present | | | |
| Eukaryota | Plantae | Spermatophyta | Bambusa vulgaris (common bamboo) | Present | | | |
| Eukaryota | Plantae | Spermatophyta | Barringtonia asiatica (sea poison tree) | Present | Native | | Govaerts & Tulig, 2014 |
| Eukaryota | Plantae | Spermatophyta | Cassia fistula (Indian laburnum) | Present | | | ILDIS, 2014; Lock & Ford, 2004 |
| Eukaryota | Plantae | Spermatophyta | Cassia javanica (pink shower) | Present | Native | | ILDIS, 2014 |
| Eukaryota | Plantae | Spermatophyta | Cassytha filiformis (love-vine) | Present | Native | | GBIF, 2014 |
| Eukaryota | Plantae | Spermatophyta | Chromolaena odorata (Siam weed) | Widespread | Introduced | Yes | Gautier, 1992b |
| Eukaryota | Plantae | Spermatophyta | Chrysopogon aciculatus (golden false beardgrass) | Present | | | Seavoy, 1975 |
| Eukaryota | Plantae | Spermatophyta | Cinnamomum burmanni (padang cassia) | Localised | Introduced | | Wuu-Kuang, 2011 |
| Eukaryota | Plantae | Spermatophyta | Cleome rutidosperma (fringed spiderflower) | Widespread | Introduced | Yes | Holm et al., 1991; Jacobs, 1960; Waterhouse & Mitchell, 1998 |
| Eukaryota | Plantae | Spermatophyta | Commelina benghalensis (wandering jew) | Present | | | Holm et al., 1979 |
| Eukaryota | Plantae | Spermatophyta | Crassocephalum crepidioides (redflower ragleaf) | Present | | | Tjitrosoedirdjo, 1987 |
| Eukaryota | Plantae | Spermatophyta | Crotalaria retusa (rattleweed) | Present | Native | | ILDIS, 2013 |
| Eukaryota | Plantae | Spermatophyta | Cyperus rotundus (purple nutsedge) | Present | Native | | Govaerts, 2014 |
| Eukaryota | Plantae | Spermatophyta | Eichhornia crassipes (water hyacinth) | Widespread | Introduced | Yes | Gopal, 1987 |
| Eukaryota | Plantae | Spermatophyta | Epipremnum pinnatum (centipede tongavine) | Present | Native | | Govaerts, 2012 |
| Eukaryota | Plantae | Spermatophyta | Eucalyptus camaldulensis (red gum) | Present | Introduced | | |
| Eukaryota | Plantae | Spermatophyta | Euphorbia heterophylla (wild poinsettia) | Present | | | |
| Eukaryota | Plantae | Spermatophyta | Euphorbia hirta (garden spurge) | Present | | | Holm et al., 1979 |
| Eukaryota | Plantae | Spermatophyta | Falcataria moluccana (batai wood) | Present | | | CABI, 2005 |
| Eukaryota | Plantae | Spermatophyta | Flemingia strobilifera (wild hops) | Present | Native | | ILDIS, 2014 |
| Eukaryota | Plantae | Spermatophyta | Gliricidia sepium (mother of cocoa) | Present | Introduced | | |
| Eukaryota | Plantae | Spermatophyta | Hibiscus tiliaceus (coast cottonwood) | Present | | | |
| Eukaryota | Plantae | Spermatophyta | Imperata cylindrica (cogon grass) | Widespread | Native | | Kostermans et al., 1987 |
| Eukaryota | Plantae | Spermatophyta | Indigofera tinctoria (true indigo) | Present | Native | | ILDIS, 2014 |
| Eukaryota | Plantae | Spermatophyta | Ischaemum rugosum (saramollagrass) | Present | | | Holm et al., 1979 |
| Eukaryota | Plantae | Spermatophyta | Ischaemum timorense (centipede grass) | Present | | | Holm et al., 1979; Gilliland et al., 1971 |
| Eukaryota | Plantae | Spermatophyta | Lantana camara (lantana) | Widespread | Introduced | Yes | Holm et al., 1979 |
| Eukaryota | Plantae | Spermatophyta | Lemna perpusilla (duckweed) | Present | | | Holm et al., 1979 |
| Eukaryota | Plantae | Spermatophyta | Leonurus japonicus (honeyweed) | Present | Native | | Govaerts, 2014 |
| Eukaryota | Plantae | Spermatophyta | Leucaena diversifolia | Present | Introduced | | |
| Eukaryota | Plantae | Spermatophyta | Leucaena leucocephala (leucaena) | Present | Introduced | | CABI, 2005 |
| Eukaryota | Plantae | Spermatophyta | Ludwigia hyssopifolia (water primrose) | Present | | | Holm et al., 1979 |
| Eukaryota | Plantae | Spermatophyta | Ludwigia octovalvis (primrose willow) | Present | | | Raven, 1963 |
| Eukaryota | Plantae | Spermatophyta | Macaranga tanarius (parasol leaf tree) | Present | Native | | Purwaningsih & Sukardjo, 1991 |
| Eukaryota | Plantae | Spermatophyta | Maesopsis eminii (umbrella tree) | Present | | | |
| Eukaryota | Plantae | Spermatophyta | Mangifera indica (mango) | Present | Introduced | | IUCN, 2013 |
| Eukaryota | Plantae | Spermatophyta | Megathyrsus maximus (Guinea grass) | Present | Introduced | | Holm et al., 1979 |
| Eukaryota | Plantae | Spermatophyta | Melastoma malabathricum (Banks melastoma) | Present | | | Hiratsuka et al., 2006 |
| Eukaryota | Plantae | Spermatophyta | Merremia peltata | Present | | | Van & Hoogland, 1953 |
| Eukaryota | Plantae | Spermatophyta | Merremia umbellata (hogvine) | Present | | | Van & Ooststroom Hoogland, 1953 |
| Eukaryota | Plantae | Spermatophyta | Mimosa diplotricha (giant sensitive plant) | Present | | | Soerjani et al., 1987 |
| Eukaryota | Plantae | Spermatophyta | Mimosa pudica (sensitive plant) | Present | Introduced | | |
| Eukaryota | Plantae | Spermatophyta | Murdannia nudiflora (doveweed) | Widespread | Introduced | Yes | Soerjani et al., 1987; Waterhouse, 1993; Galinato et al., 1999; Holm et al., 1977 |
| Eukaryota | Plantae | Spermatophyta | Nypa fruticans (nipa palm) | Widespread | Native | | Sukanda, 1995 |
| Eukaryota | Plantae | Spermatophyta | Oryza rufipogon (wild rice) | Present | | | Chang, 1975 |
| Eukaryota | Plantae | Spermatophyta | Paederia foetida (skunkvine) | Present | Native | | Flora of China Editorial Committee, 2015 |
| Eukaryota | Plantae | Spermatophyta | Panicum repens (torpedo grass) | Present | Introduced | | Soerjani et al., 1987 |
| Eukaryota | Plantae | Spermatophyta | Paspalum conjugatum (sour paspalum) | Widespread | | | Holm et al., 1979 |
| Eukaryota | Plantae | Spermatophyta | Peltophorum pterocarpum (copperpod) | Present | | | |
| Eukaryota | Plantae | Spermatophyta | Pennisetum polystachion (mission grass) | Localised | Introduced | | Chiu & Chee, 1998 |
| Eukaryota | Plantae | Spermatophyta | Phyllanthus urinaria (leafflower) | Widespread | Native | Yes | Soerjani et al., 1987; Moody, 1989 |
| Eukaryota | Plantae | Spermatophyta | Piper aduncum (spiked pepper) | Widespread | Introduced | Yes | Padmanaba & Sheil, 2014 |
| Eukaryota | Plantae | Spermatophyta | Pistia stratiotes (water lettuce) | Widespread | | | |
| Eukaryota | Plantae | Spermatophyta | Pithecellobium dulce (Manila tamarind) | Present | Introduced | | |
| Eukaryota | Plantae | Spermatophyta | Poa annua (annual meadowgrass) | Present | | | Holm et al., 1991 |
| Eukaryota | Plantae | Spermatophyta | Portulaca oleracea (purslane) | Present | | | Holm et al., 1991 |
| Eukaryota | Plantae | Spermatophyta | Psidium guajava (guava) | Present | Introduced | | Govaerts, 2013 |
| Eukaryota | Plantae | Spermatophyta | Ricinus communis (castor bean) | Present | | | |
| Eukaryota | Plantae | Spermatophyta | Rubus rosifolius (roseleaf raspberry) | Present | Native | | USDA-ARS, 2014 |
| Eukaryota | Plantae | Spermatophyta | Samanea saman (rain tree) | Present | Introduced | | |
| Eukaryota | Plantae | Spermatophyta | Senna siamea (yellow cassia) | Present | Native | | ILDIS, 2007 |
| Eukaryota | Plantae | Spermatophyta | Sesbania sesban (sesban) | Present | | | |
| Eukaryota | Plantae | Spermatophyta | Spathodea campanulata (African tulip tree) | Present | | | CABI, 2005 |
| Eukaryota | Plantae | Spermatophyta | Striga asiatica (witch weed) | Present | Native | | Kostermans et al., 1987 |
| Eukaryota | Plantae | Spermatophyta | Taeniatherum caput-medusae (medusahead wildrye) | Present | Native | | Frederiksen, 1986; Missouri Botanical Garden, 2015 |
| Eukaryota | Plantae | Spermatophyta | Terminalia catappa (Singapore almond) | Present | | | |
| Eukaryota | Plantae | Spermatophyta | Xyris complanata (yellow-eyed grass) | Present | Native | | GBIF, 2015 |
| Eukaryota | Plantae | Spermatophyta | Zingiber montanum (cassumunar ginger) | Present | Introduced | | Govaerts, 2013 |
| Eukaryota | Plantae | Spermatophyta | Zingiber zerumbet (shampoo ginger) | Present | Native | | Govaerts, 2013 |
| Virus | | | Banana bunchy top virus (bunchy top of banana) | Present | | Yes | Sulyo & Muharam, 1985; EPPO, 2014; CABI/EPPO, 2013 |