| photobacterium damselae | 24 | species | bacteria | bacteria | 38293 |
| phoma oculo-hominis | 1 | species | | fungi | |
| phoma minutella | 1 | species | | fungi | |
| phoma hibernica | 2 | species | | fungi | |
| phoma herbarum | 15 | species | plants | fungi | 73001 |
| phoma eupyrena | 3 | species | plants | fungi | 297020 |
| phoma cruris-hominis | -3 | species | | fungi | |
| phnom penh bat virus | 1 | species | viruses | viruses | 64894 |
| philophthalmus lacrymosus | -3 | species | | helminths | |
| phialophora verrucosa | 16 | species | plants | fungi | 39412 |
| phialophora bubakii | 1 | species | plants | fungi | 91933 |
| phialemonium obovatum | 6 | species | plants | fungi | 291973 |
| phaneropsolus bonnei | 5 | species | | helminths | |
| phaeotrichoconis crotalariae | 2 | species | plants | fungi | 179659 |
| phaeosclera dematioides | 7 | species | plants | fungi | 71661 |
| phaeoannellomyces elegans | 4 | species | plants | fungi | 66226 |
| phaeoanellomyces werneckii | -3 | species | | fungi | |
| peptostreptococcus anaerobius | 23 | species | bacteria | bacteria | 1261 |
| peptoniphilus asaccharolyticus | 34 | species | bacteria | bacteria | 1258 |
| peptococcus niger | 8 | species | bacteria | bacteria | 2741 |
| pentatrichomonas hominis | 17 | species | invertebrates | protozoa | 5728 |
| penicillium expansum | 46 | species | plants | fungi | 27334 |
| penicillium dupontii | 1 | species | | fungi | |
| penicillium decumbens | 14 | species | plants | fungi | 69771 |
| penicillium commune | 18 | species | plants | fungi | 36653 |
| penicillium citrinum | 40 | species | plants | fungi | 5077 |
| penicillium chrysogenum | 74 | species | plants | fungi | 5076 |
| pelodera strongyloides | 9 | species | invertebrates | helminths | 35557 |
| pasteurella stomatis | 7 | species | bacteria | bacteria | 760 |
| pasteurella multocida | 65 | species | bacteria | bacteria | 747 |
| pasteurella dagmatis | 10 | species | bacteria | bacteria | 754 |
| pasteurella canis | 10 | species | bacteria | bacteria | 753 |
| pasteurella caballi | 6 | species | bacteria | bacteria | 243701 |
| parvimonas micra | 42 | species | bacteria | bacteria | 33033 |
| parengyodontium album | 29 | species | plants | fungi | 37998 |
| parascaris equorum | 25 | species | invertebrates | helminths | 6256 |
| paragonimus westermani | 20 | species | invertebrates | helminths | 34504 |
| paragonimus uterobilateralis | 8 | species | | helminths | |
| paragonimus skrjabini | 4 | species | invertebrates | helminths | 59630 |
| paragonimus siamensis | 1 | species | invertebrates | helminths | 100271 |
| paragonimus sadoensis | 1 | species | invertebrates | helminths | 62814 |
| paragonimus ohirai | 13 | species | invertebrates | helminths | 59629 |
| paragonimus miyazakii | 6 | species | invertebrates | helminths | 59628 |
| paragonimus mexicanus | 5 | species | invertebrates | helminths | 100270 |
| paragonimus kellicotti | 10 | species | invertebrates | helminths | 100269 |
| paragonimus hueitungensis | 1 | species | | helminths | |
| paragonimus heterotremus | 9 | species | invertebrates | helminths | 100268 |
| paragonimus caliensis | 2 | species | | helminths | 1902345 |
| paragonimus bangkokensis | 2 | species | invertebrates | helminths | 362703 |
| paragonimus africanus | 5 | species | invertebrates | helminths | 434055 |
| paraconiothyrium fuckelii | 4 | species | plants | fungi | 135648 |
| paracoccidioides brasiliensis | 53 | species | plants | fungi | 121759 |
| paraclostridium bifermentans | 26 | species | bacteria | bacteria | 1490 |
| parabacteroides merdae | 7 | species | bacteria | bacteria | 46503 |
| parabacteroides distasonis | 24 | species | bacteria | bacteria | 823 |
| pantoea agglomerans | 63 | species | bacteria | bacteria | 549 |
| paeniclostridium sordellii | 38 | species | bacteria | bacteria | 1505 |
| paenibacillus macerans | 27 | species | bacteria | bacteria | 44252 |
| paenibacillus alvei | 19 | species | bacteria | bacteria | 44250 |
| paecilomyces fumerosoreus | -3 | species | | fungi | |
| ovadendron sulphureo-ochraceum | 5 | species | | fungi | |
| ovadendron ochraceum | -3 | species | | fungi | |
| ostertagia ostertagi | 46 | species | invertebrates | helminths | 6317 |
| orungo virus | 4 | species | | viruses | 40058 |
| oropouche virus | 11 | species | viruses | viruses | 118655 |
| ornithobilharzia | 8 | genus | invertebrates | | 100597 |
| orientia tsutsugamushi | 40 | species | bacteria | bacteria | 784 |
| oriboca virus | 3 | species | viruses | viruses | 192199 |
| orf virus | 38 | species | viruses | viruses | 10258 |
| oran virus | -3 | no rank | viruses | viruses | 69247 |
| opisthorchis viverrini | 40 | species | invertebrates | helminths | 6198 |
| opisthorchis sinensis | 1 | species | invertebrates | helminths | 41765 |
| opisthorchis noverca | 3 | species | | helminths | 1269762 |
| opisthorchis guayaquilensis | -3 | species | | helminths | |
| opisthorchis felineus | 10 | species | invertebrates | helminths | 147828 |
| onchocerca volvulus | 64 | species | invertebrates | helminths | 6282 |
| omsk hemorrhagic fever virus | 8 | species | viruses | viruses | 12542 |
| oligella urethralis | 12 | species | bacteria | bacteria | 90245 |
| oligella ureolytica | 3 | species | bacteria | bacteria | 90244 |
| oidiodendron cerealis | 2 | species | plants | fungi | 78142 |
| oesophagostomum stephanostomum | 5 | species | invertebrates | helminths | 92252 |
| oesophagostomum bifurcum | 17 | species | invertebrates | helminths | 61179 |
| oerskovia turbata | 8 | species | bacteria | bacteria | 1713 |
| odoribacter splanchnicus | 4 | species | bacteria | bacteria | 28118 |
| ockelbo virus | 14 | no rank | viruses | viruses | 31699 |
| ochroconis tshawytschae | 2 | species | plants | fungi | 262132 |
| ochroconis humicola | 7 | species | plants | fungi | 228895 |
| ochrocladosporium elatum | 1 | species | plants | fungi | 652621 |
| ochrobactrum anthropi | 32 | species | bacteria | bacteria | 529 |
| nyando virus | 1 | no rank | viruses | viruses | 35316 |
| nosema ocularum | 1 | species | | fungi | |
| nosema connori | 4 | species | | fungi | |
| nosema ceylonensis | -3 | species | | fungi | |
| nosema africanum | -3 | species | | fungi | |
| norwalk virus | 73 | species | viruses | viruses | 11983 |
| nocardia transvalensis | 10 | species | bacteria | bacteria | 37333 |
| nocardia pseudobrasiliensis | 8 | species | bacteria | bacteria | 45979 |
| nocardia otitidiscaviarum | 17 | species | bacteria | bacteria | 1823 |
| nocardia nova | 13 | species | bacteria | bacteria | 37330 |
| nocardia farcinica | 23 | species | bacteria | bacteria | 37329 |