| fibricola seoulensis | 1 | species | | helminths | |
| fibrobacter intestinalis | 9 | species | bacteria | bacteria | 28122 |
| filifactor alocis | 16 | species | bacteria | bacteria | 143361 |
| finegoldia magna | 28 | species | bacteria | bacteria | 1260 |
| fluoribacter bozemanae | 16 | species | bacteria | bacteria | 447 |
| fluoribacter dumoffii | 11 | species | bacteria | bacteria | 463 |
| fluoribacter gormanii | 14 | species | bacteria | bacteria | 464 |
| fonsecaea compacta | 7 | species | plants | fungi | 86057 |
| fonsecaea pedrosoi | 28 | species | plants | fungi | 40355 |
| foot-and-mouth disease virus | 89 | species | viruses | viruses | 12110 |
| francisella tularensis | 74 | species | bacteria | bacteria | 263 |
| fusarium aquaeductuum | 10 | species | plants | fungi | 595638 |
| fusarium chlamydosporum | 13 | species | plants | fungi | 86545 |
| fusarium dimerum | 9 | species | plants | fungi | 57145 |
| fusarium falciforme | 9 | species | plants | fungi | 195108 |
| fusarium incarnatum | 17 | species | plants | fungi | 298378 |
| fusarium lichenicola | 12 | species | plants | fungi | 42744 |
| fusarium napiforme | 5 | species | plants | fungi | 42672 |
| fusarium oxysporum | 93 | species | plants | fungi | 5507 |
| fusarium sacchari | 7 | species | plants | fungi | 42676 |
| fusarium solani | 73 | species | plants | fungi | 169388 |
| fusarium subglutinans | 30 | species | plants | fungi | 42677 |
| fusarium ventricosum | 3 | species | plants | fungi | 42327 |
| fusarium verticillioides | 97 | species | plants | fungi | 117187 |
| fusobacterium mortiferum | 20 | species | bacteria | bacteria | 850 |
| fusobacterium necrophorum | 40 | species | bacteria | bacteria | 859 |
| fusobacterium nucleatum | 61 | species | bacteria | bacteria | 851 |
| fusobacterium periodonticum | 12 | species | bacteria | bacteria | 860 |
| fusobacterium ulcerans | 7 | species | bacteria | bacteria | 861 |
| fusobacterium varium | 18 | species | bacteria | bacteria | 856 |
| gan gan virus | 2 | species | | viruses | 1764076 |
| gardnerella vaginalis | 52 | species | bacteria | bacteria | 2702 |
| gastrodiscoides hominis | 5 | species | invertebrates | helminths | 408852 |
| gb virus c | 69 | species | viruses | viruses | 54290 |
| gemella morbillorum | 18 | species | bacteria | bacteria | 29391 |
| getah virus | 11 | species | viruses | viruses | 59300 |
| giardia intestinalis | 53 | species | invertebrates | protozoa | 5741 |
| gibellulopsis nigrescens | 7 | species | plants | fungi | 796325 |
| gigantobilharzia huttoni | 1 | species | | helminths | |
| gigantobilharzia sturniae | -3 | species | | helminths | |
| gnathostoma doloresi | 5 | species | invertebrates | helminths | 279402 |
| gnathostoma hispidum | 4 | species | invertebrates | helminths | 279404 |
| gnathostoma nipponicum | 5 | species | invertebrates | helminths | 279403 |
| gnathostoma spinigerum | 15 | species | invertebrates | helminths | 75299 |
| gongylonema pulchrum | 6 | species | invertebrates | helminths | 637853 |
| gordonia amarae | 22 | species | bacteria | bacteria | 36821 |
| gordonia bronchialis | 10 | species | bacteria | bacteria | 2054 |
| gordonia rubripertincta | 32 | species | bacteria | bacteria | 36822 |
| gordonia sputi | 7 | species | bacteria | bacteria | 36823 |
| gordonia terrae | 10 | species | bacteria | bacteria | 2055 |
| granulicatella adiacens | 17 | species | bacteria | bacteria | 46124 |
| grimontia hollisae | 18 | species | bacteria | bacteria | 673 |
| guanarito mammarenavirus | 15 | species | viruses | viruses | 45219 |
| guaroa virus | 8 | species | viruses | viruses | 80941 |
| gymnophalloides | 9 | genus | invertebrates | helminths | 87179 |
| haemonchus contortus | 74 | species | invertebrates | helminths | 6289 |
| haemophilus haemolyticus | 14 | species | bacteria | bacteria | 726 |
| haemophilus influenzae | 148 | species | bacteria | bacteria | 727 |
| haemophilus parahaemolyticus | 24 | species | bacteria | bacteria | 735 |
| haemophilus parainfluenzae | 30 | species | bacteria | bacteria | 729 |
| hafnia alvei | 39 | species | bacteria | bacteria | 569 |
| hantaan virus | 61 | species | viruses | viruses | 11599 |
| haplorchis pumilio | 9 | species | invertebrates | helminths | 235154 |
| haplorchis taichui | 9 | species | invertebrates | helminths | 235153 |
| haplorchis vanissima | -3 | species | | helminths | |
| haplorchis yokogawai | 3 | species | invertebrates | helminths | 667377 |
| hathewaya histolytica | 40 | species | bacteria | bacteria | 1498 |
| helicobacter cinaedi | 27 | species | bacteria | bacteria | 213 |
| helicobacter fennelliae | 16 | species | bacteria | bacteria | 215 |
| helicobacter heilmannii | 37 | species | bacteria | bacteria | 35817 |
| helicobacter pullorum | 19 | species | bacteria | bacteria | 35818 |
| helicobacter pylori | 246 | species | bacteria | bacteria | 210 |
| hendra virus | 43 | species | viruses | viruses | 63330 |
| hepatitis b virus | 246 | species | viruses | viruses | 10407 |
| hepatitis c virus | 289 | species | viruses | viruses | 11103 |
| hepatitis delta virus | 89 | species | viruses | viruses | 12475 |
| hepatovirus a | 95 | species | viruses | viruses | 12092 |
| heterobilharzia americana | 11 | species | invertebrates | helminths | 39320 |
| heterophyes dispar | 1 | species | | helminths | |
| heterophyes heterophyes | 4 | species | | helminths | 1849833 |
| heterophyes nocens | 3 | species | invertebrates | helminths | 104455 |
| heterophyopsis continua | 3 | species | | helminths | 1193295 |
| himasthla muehlensi | -3 | species | | helminths | |
| histoplasma capsulatum | 72 | species | plants | fungi | 5037 |
| hortaea werneckii | 16 | species | plants | fungi | 91943 |
| hu39694 virus | -3 | no rank | viruses | viruses | 69244 |
| hughes virus | 4 | species | viruses | viruses | 248052 |
| human coronavirus 229e | 39 | species | viruses | viruses | 11137 |
| human coronavirus oc43 | 29 | no rank | viruses | viruses | 31631 |
| human herpesvirus 1 | 171 | species | viruses | viruses | 10298 |
| human herpesvirus 2 | 96 | species | viruses | viruses | 10310 |
| human herpesvirus 3 | 113 | species | viruses | viruses | 10335 |
| human herpesvirus 4 | 257 | species | viruses | viruses | 10376 |
| human herpesvirus 5 | 159 | species | viruses | viruses | 10359 |
| human herpesvirus 6 | 94 | species | viruses | viruses | 10368 |
| human herpesvirus 7 | 48 | species | viruses | viruses | 10372 |
| human herpesvirus 8 | 140 | species | viruses | viruses | 37296 |
| human immunodeficiency virus 1 | 410 | species | viruses | viruses | 11676 |
| human immunodeficiency virus 2 | 399 | species | viruses | viruses | 11709 |
| human mastadenovirus a | 1 | species | viruses | viruses | 129875 |