| ross river virus | 48 | species | viruses | viruses | 11029 |
| rinderpest virus | 39 | species | viruses | viruses | 11241 |
| rift valley fever virus | 41 | species | viruses | viruses | 11588 |
| rickettsia typhi | 36 | species | bacteria | bacteria | 785 |
| rickettsia rickettsii | 53 | species | bacteria | bacteria | 783 |
| rickettsia prowazekii | 51 | species | bacteria | bacteria | 782 |
| rickettsia felis | 29 | species | bacteria | bacteria | 42862 |
| rickettsia conorii | 40 | species | bacteria | bacteria | 781 |
| ricinus communis | 104 | species | plants | | 3988 |
| rice yellow mottle virus | 23 | species | viruses | viruses | 31744 |
| rice tungro bacilliform virus | 21 | species | viruses | viruses | 10654 |
| rice stripe virus | 118 | species | viruses | viruses | 12331 |
| rice ragged stunt virus | 15 | species | viruses | viruses | 42475 |
| rice gall dwarf virus | 11 | species | viruses | viruses | 10986 |
| rice dwarf virus | 29 | species | viruses | viruses | 10991 |
| rice black streaked dwarf virus | 14 | species | viruses | viruses | 10990 |
| rhodococcus equi | 50 | species | bacteria | bacteria | 43767 |
| rhizopus oryzae | 86 | species | plants | fungi | 64495 |
| rhinovirus b | 8 | species | viruses | viruses | 147712 |
| rhinovirus a | 7 | species | viruses | viruses | 147711 |
| reston ebolavirus | 9 | species | viruses | viruses | 186539 |
| recombinant sars coronavirus | 3 | species | synthetic | | 575560 |
| ralstonia solanacearum | 79 | species | bacteria | bacteria | 305 |
| ralstonia pickettii | 44 | species | bacteria | bacteria | 329 |
| ralstonia mannitolilytica | 9 | species | bacteria | bacteria | 105219 |
| rabies virus | 96 | species | viruses | viruses | 11292 |
| rabbitpox virus | 31 | no rank | viruses | viruses | 32606 |
| rabbit hemorrhagic disease virus | 37 | species | viruses | viruses | 11976 |
| pyrodinium bahamense | 16 | species | plants | protozoa | 73915 |
| pseudomonas stutzeri | 76 | species | bacteria | bacteria | 316 |
| pseudomonas savastanoi pv. glycinea | 35 | no rank | bacteria | bacteria | 318 |
| pseudomonas putida | 133 | species | bacteria | bacteria | 303 |
| pseudomonas fluorescens | 122 | species | bacteria | bacteria | 294 |
| pseudomonas alcaligenes | 25 | species | bacteria | bacteria | 43263 |
| pseudomonas aeruginosa | 243 | species | bacteria | bacteria | 287 |
| pseudoalteromonas tetraodonis | 9 | species | bacteria | bacteria | 43659 |
| providencia stuartii | 41 | species | bacteria | bacteria | 588 |
| proteus vulgaris | 53 | species | bacteria | bacteria | 585 |
| proteus mirabilis | 80 | species | bacteria | bacteria | 584 |
| propionibacterium acnes | 77 | species | bacteria | bacteria | 1747 |
| powassan virus | 11 | species | viruses | viruses | 11083 |
| potato virus y | 52 | species | viruses | viruses | 12216 |
| potato virus x | 71 | species | viruses | viruses | 12183 |
| pneumocystis jirovecii | 34 | species | plants | fungi | 42068 |
| plum pox virus | 57 | species | viruses | viruses | 12211 |
| plasmodium vivax | 80 | species | invertebrates | protozoa | 5855 |
| plasmodium falciparum | 209 | species | invertebrates | protozoa | 5833 |
| pichia kudriavzevii | 67 | species | plants | fungi | 4909 |
| phyllobates terribilis | 2 | species | vertebrates | | 111132 |
| phakopsora pachyrhizi | 32 | species | plants | fungi | 170000 |
| peste-des-petits-ruminants virus | 32 | species | viruses | viruses | 31604 |
| peronosclerospora philippinensis | 4 | species | plants | | 886948 |
| peptostreptococcus anaerobius | 23 | species | bacteria | bacteria | 1261 |
| peptococcus niger | 8 | species | bacteria | bacteria | 2741 |
| pasteurella multocida | 65 | species | bacteria | bacteria | 747 |
| parachlamydia acanthamoebae | 20 | species | bacteria | bacteria | 83552 |
| oropouche virus | 11 | species | viruses | viruses | 118655 |
| orientia tsutsugamushi | 40 | species | bacteria | bacteria | 784 |
| oran virus | -3 | no rank | viruses | viruses | 69247 |
| omsk hemorrhagic fever virus | 8 | species | viruses | viruses | 12542 |
| norwalk virus | 73 | species | viruses | viruses | 11983 |
| northern cereal mosaic virus | 4 | species | viruses | viruses | 100880 |
| nocardia nova | 13 | species | bacteria | bacteria | 37330 |
| nocardia asteroides | 51 | species | bacteria | bacteria | 1824 |
| nipah virus | 51 | species | viruses | viruses | 121791 |
| nicotiana tabacum | 304 | species | plants | | 4097 |
| newcastle disease virus | 93 | species | viruses | viruses | 11176 |
| new york virus | 7 | species | viruses | viruses | 44755 |
| neorickettsia sennetsu | 18 | species | bacteria | bacteria | 951 |
| neisseria meningitidis | 130 | species | bacteria | bacteria | 487 |
| neisseria gonorrhoeae | 136 | species | bacteria | bacteria | 485 |
| nectria haematococca | 50 | species | plants | fungi | 140110 |
| naegleria fowleri | 33 | species | invertebrates | protozoa | 5763 |
| mycoplasma pneumoniae | 93 | species | bacteria | bacteria | 2104 |
| mycoplasma mycoides | 38 | species | bacteria | bacteria | 2102 |
| mycoplasma capricolum subsp. capripneumoniae | 11 | subspecies | bacteria | bacteria | 40480 |
| mycoplasma capricolum | 43 | species | bacteria | bacteria | 2095 |
| mycobacterium xenopi | 34 | species | bacteria | bacteria | 1789 |
| mycobacterium ulcerans | 46 | species | bacteria | bacteria | 1809 |
| mycobacterium szulgai | 18 | species | bacteria | bacteria | 1787 |
| mycobacterium simiae | 25 | species | bacteria | bacteria | 1784 |
| mycobacterium scrofulaceum | 31 | species | bacteria | bacteria | 1783 |
| mycobacterium marinum | 51 | species | bacteria | bacteria | 1781 |
| mycobacterium leprae | 95 | species | bacteria | bacteria | 1769 |
| mycobacterium kansasii | 49 | species | bacteria | bacteria | 1768 |
| mycobacterium haemophilum | 26 | species | bacteria | bacteria | 29311 |
| mycobacterium fortuitum | 60 | species | bacteria | bacteria | 1766 |
| mycobacterium bovis | 132 | species | bacteria | bacteria | 1765 |
| mycobacterium avium | 125 | species | bacteria | bacteria | 1764 |
| mycobacterium abscessus | 38 | species | bacteria | bacteria | 36809 |
| murray valley encephalitis virus | 28 | species | viruses | viruses | 11079 |
| mumps virus | 61 | species | viruses | viruses | 11161 |
| mucor circinelloides | 27 | species | plants | fungi | 36080 |
| morganella morganii | 46 | species | bacteria | bacteria | 582 |
| moraxella catarrhalis | 87 | species | bacteria | bacteria | 480 |
| monkeypox virus | 35 | species | viruses | viruses | 10244 |
| molluscum contagiosum virus | 36 | species | viruses | viruses | 10279 |
| menangle virus | 12 | species | viruses | viruses | 152219 |
| measles virus | 119 | species | viruses | viruses | 11234 |
| marburg marburgvirus | 17 | species | viruses | viruses | 11269 |