| haplorchis vanissima | -3 | species | | helminths | |
| haplorchis taichui | 9 | species | invertebrates | helminths | 235153 |
| haplorchis pumilio | 9 | species | invertebrates | helminths | 235154 |
| hantaan virus | 61 | species | viruses | viruses | 11599 |
| hafnia alvei | 39 | species | bacteria | bacteria | 569 |
| haemophilus parainfluenzae | 30 | species | bacteria | bacteria | 729 |
| haemophilus parahaemolyticus | 24 | species | bacteria | bacteria | 735 |
| haemophilus influenzae | 148 | species | bacteria | bacteria | 727 |
| haemophilus haemolyticus | 14 | species | bacteria | bacteria | 726 |
| haemonchus contortus | 74 | species | invertebrates | helminths | 6289 |
| gymnophalloides | 9 | genus | invertebrates | helminths | 87179 |
| guaroa virus | 8 | species | viruses | viruses | 80941 |
| guanarito mammarenavirus | 15 | species | viruses | viruses | 45219 |
| grimontia hollisae | 18 | species | bacteria | bacteria | 673 |
| granulicatella adiacens | 17 | species | bacteria | bacteria | 46124 |
| gordonia terrae | 10 | species | bacteria | bacteria | 2055 |
| gordonia sputi | 7 | species | bacteria | bacteria | 36823 |
| gordonia rubripertincta | 32 | species | bacteria | bacteria | 36822 |
| gordonia bronchialis | 10 | species | bacteria | bacteria | 2054 |
| gordonia amarae | 22 | species | bacteria | bacteria | 36821 |
| gongylonema pulchrum | 6 | species | invertebrates | helminths | 637853 |
| gnathostoma spinigerum | 15 | species | invertebrates | helminths | 75299 |
| gnathostoma nipponicum | 5 | species | invertebrates | helminths | 279403 |
| gnathostoma hispidum | 4 | species | invertebrates | helminths | 279404 |
| gnathostoma doloresi | 5 | species | invertebrates | helminths | 279402 |
| gigantobilharzia sturniae | -3 | species | | helminths | |
| gigantobilharzia huttoni | 1 | species | | helminths | |
| gibellulopsis nigrescens | 7 | species | plants | fungi | 796325 |
| giardia intestinalis | 53 | species | invertebrates | protozoa | 5741 |
| getah virus | 11 | species | viruses | viruses | 59300 |
| gemella morbillorum | 18 | species | bacteria | bacteria | 29391 |
| gb virus c | 69 | species | viruses | viruses | 54290 |
| gastrodiscoides hominis | 5 | species | invertebrates | helminths | 408852 |
| gardnerella vaginalis | 52 | species | bacteria | bacteria | 2702 |
| gan gan virus | 2 | species | | viruses | 1764076 |
| fusobacterium varium | 18 | species | bacteria | bacteria | 856 |
| fusobacterium ulcerans | 7 | species | bacteria | bacteria | 861 |
| fusobacterium periodonticum | 12 | species | bacteria | bacteria | 860 |
| fusobacterium nucleatum | 61 | species | bacteria | bacteria | 851 |
| fusobacterium necrophorum | 40 | species | bacteria | bacteria | 859 |
| fusobacterium mortiferum | 20 | species | bacteria | bacteria | 850 |
| fusarium verticillioides | 97 | species | plants | fungi | 117187 |
| fusarium ventricosum | 3 | species | plants | fungi | 42327 |
| fusarium subglutinans | 30 | species | plants | fungi | 42677 |
| fusarium solani | 73 | species | plants | fungi | 169388 |
| fusarium sacchari | 7 | species | plants | fungi | 42676 |
| fusarium oxysporum | 93 | species | plants | fungi | 5507 |
| fusarium napiforme | 5 | species | plants | fungi | 42672 |
| fusarium lichenicola | 12 | species | plants | fungi | 42744 |
| fusarium incarnatum | 17 | species | plants | fungi | 298378 |
| fusarium falciforme | 9 | species | plants | fungi | 195108 |
| fusarium dimerum | 9 | species | plants | fungi | 57145 |
| fusarium chlamydosporum | 13 | species | plants | fungi | 86545 |
| fusarium aquaeductuum | 10 | species | plants | fungi | 595638 |
| francisella tularensis | 74 | species | bacteria | bacteria | 263 |
| foot-and-mouth disease virus | 89 | species | viruses | viruses | 12110 |
| fonsecaea pedrosoi | 28 | species | plants | fungi | 40355 |
| fonsecaea compacta | 7 | species | plants | fungi | 86057 |
| fluoribacter gormanii | 14 | species | bacteria | bacteria | 464 |
| fluoribacter dumoffii | 11 | species | bacteria | bacteria | 463 |
| fluoribacter bozemanae | 16 | species | bacteria | bacteria | 447 |
| finegoldia magna | 28 | species | bacteria | bacteria | 1260 |
| filifactor alocis | 16 | species | bacteria | bacteria | 143361 |
| fibrobacter intestinalis | 9 | species | bacteria | bacteria | 28122 |
| fibricola seoulensis | 1 | species | | helminths | |
| fasciolopsis buski | 11 | species | invertebrates | helminths | 27845 |
| fasciola indica | 3 | species | | helminths | |
| fasciola hepatica | 68 | species | invertebrates | helminths | 6192 |
| fasciola gigantica | 23 | species | invertebrates | helminths | 46835 |
| far eastern tick-borne encephalitis virus | 1 | no rank | | viruses | |
| falciformispora tompkinsii | 2 | species | plants | fungi | 1489896 |
| faecalitalea cylindroides | 4 | species | bacteria | bacteria | 39483 |
| eyach virus | 8 | species | viruses | viruses | 62352 |
| exserohilum mcginnisii | 1 | species | plants | fungi | 91494 |
| exserohilum longirostratum | 3 | species | plants | fungi | 132106 |
| exophiala spinifera | 17 | species | plants | fungi | 91928 |
| exophiala salmonis | 4 | species | plants | fungi | 43214 |
| exophiala psychrophila | 1 | species | plants | fungi | 91927 |
| exophiala pisciphila | 8 | species | plants | fungi | 86051 |
| exophiala moniliae | 5 | species | plants | fungi | 91926 |
| exophiala jeanselmei | 26 | species | plants | fungi | 5584 |
| exophiala dermatitidis | 42 | species | plants | fungi | 5970 |
| ewingella americana | 10 | species | bacteria | bacteria | 41202 |
| eustrongylides | 15 | genus | invertebrates | | 513041 |
| eurytrema pancreaticum | 5 | species | invertebrates | helminths | 374591 |
| european bat lyssavirus 2 | 14 | species | viruses | viruses | 57483 |
| european bat lyssavirus 1 | 19 | species | viruses | viruses | 57482 |
| eucoleus aerophilus | 7 | species | | helminths | 1237089 |
| eubacterium multiforme | 2 | species | bacteria | bacteria | 83339 |
| eubacterium limosum | 27 | species | bacteria | bacteria | 1736 |
| escherichia coli | 524 | species | bacteria | bacteria | 562 |
| erysipelothrix rhusiopathiae | 28 | species | bacteria | bacteria | 1648 |
| erysipelatoclostridium ramosum | 16 | species | bacteria | bacteria | 1547 |
| episthmium caninum | -3 | species | | helminths | |
| epidermophyton floccosum | 29 | species | plants | fungi | 34391 |
| enterovirus d70 | 24 | no rank | viruses | viruses | 12090 |
| enterovirus d68 | 8 | no rank | viruses | viruses | 42789 |
| enterovirus d | 5 | species | viruses | viruses | 138951 |
| enterovirus c | 118 | species | viruses | viruses | 138950 |
| enterovirus b | 16 | species | viruses | viruses | 138949 |