| zinga virus | 3 | species | | viruses | |
| zika virus | 11 | species | viruses | viruses | 64320 |
| zaire ebolavirus | 20 | species | viruses | viruses | 186538 |
| yogue virus | -3 | species | | viruses | 1712572 |
| yersinia ruckeri | 36 | species | bacteria | bacteria | 29486 |
| yersinia rohdei | 3 | species | bacteria | bacteria | 29485 |
| yersinia pseudotuberculosis | 99 | species | bacteria | bacteria | 633 |
| yersinia pestis | 105 | species | bacteria | bacteria | 632 |
| yersinia mollaretii | 4 | species | bacteria | bacteria | 33060 |
| yersinia kristensenii | 11 | species | bacteria | bacteria | 28152 |
| yersinia intermedia | 12 | species | bacteria | bacteria | 631 |
| yersinia frederiksenii | 11 | species | bacteria | bacteria | 29484 |
| yersinia enterocolitica | 126 | species | bacteria | bacteria | 630 |
| yersinia bercovieri | 5 | species | bacteria | bacteria | 634 |
| yellow fever virus | 83 | species | viruses | viruses | 11089 |
| yarrowia lipolytica | 63 | species | plants | fungi | 4952 |
| yaba monkey tumor virus | 9 | species | viruses | viruses | 38804 |
| wyeomyia virus | 1 | species | viruses | viruses | 273350 |
| wuchereria lewisi | 1 | species | | helminths | |
| wuchereria bancrofti | 52 | species | invertebrates | helminths | 6293 |
| wolinella succinogenes | 58 | species | bacteria | bacteria | 844 |
| wickerhamomyces anomalus | 41 | species | plants | fungi | 4927 |
| western equine encephalitis virus | 30 | species | viruses | viruses | 11039 |
| west nile virus | 97 | species | viruses | viruses | 11082 |
| wesselsbron virus | 5 | species | viruses | viruses | 164416 |
| watsonius watsoni | 1 | species | invertebrates | helminths | 758770 |
| wanowrie virus | 1 | species | | viruses | |
| wad medani virus | -3 | species | | viruses | 40067 |
| volutella cinerescens | -3 | species | | fungi | |
| vittaforma corneae | 18 | species | plants | fungi | 42399 |
| vibrio vulnificus | 73 | species | bacteria | bacteria | 672 |
| vibrio parahaemolyticus | 74 | species | bacteria | bacteria | 670 |
| vibrio mimicus | 28 | species | bacteria | bacteria | 674 |
| vibrio furnissii | 25 | species | bacteria | bacteria | 29494 |
| vibrio fluvialis | 23 | species | bacteria | bacteria | 676 |
| vibrio cincinnatiensis | 5 | species | bacteria | bacteria | 675 |
| vibrio cholerae | 145 | species | bacteria | bacteria | 666 |
| vibrio alginolyticus | 56 | species | bacteria | bacteria | 663 |
| vesicular stomatitis virus | 177 | species | viruses | viruses | 11276 |
| verruconis gallopava | 15 | species | plants | fungi | 253628 |
| veronaea botryosa | 4 | species | plants | fungi | 364773 |
| venezuelan equine encephalitis virus (strain everglades fe3-7c) | -3 | no rank | viruses | viruses | 36383 |
| venezuelan equine encephalitis virus | 54 | species | viruses | viruses | 11036 |
| veillonella parvula | 36 | species | bacteria | bacteria | 29466 |
| veillonella dispar | 17 | species | bacteria | bacteria | 39778 |
| veillonella atypica | 12 | species | bacteria | bacteria | 39777 |
| variola virus | 80 | species | viruses | viruses | 10255 |
| variant creutzfeldt-jakob disease agent | 31 | species | | | |
| usutu virus | 15 | species | viruses | viruses | 64286 |
| ureaplasma urealyticum | 70 | species | bacteria | bacteria | 2130 |
| uncinaria stenocephala | 17 | species | invertebrates | helminths | 125367 |
| tyuleniy virus | 2 | species | viruses | viruses | 40004 |
| tubercularia vulgaris | 4 | species | plants | fungi | 29877 |
| tsukamurella tyrosinosolvens | 4 | species | bacteria | bacteria | 57704 |
| tsukamurella pulmonis | 5 | species | bacteria | bacteria | 47312 |
| tsukamurella paurometabola | 20 | species | bacteria | bacteria | 2061 |
| tsukamurella inchonensis | 6 | species | bacteria | bacteria | 42777 |
| trypanosoma cruzi | 130 | species | invertebrates | protozoa | 5693 |
| trypanosoma brucei | 133 | species | invertebrates | protozoa | 5691 |
| trueperella pyogenes | 37 | species | bacteria | bacteria | 1661 |
| trueperella bernardiae | 8 | species | bacteria | bacteria | 59561 |
| trubanaman virus | 2 | species | | viruses | 1678230 |
| tropheryma whipplei | 41 | species | bacteria | bacteria | 2039 |
| tritirachium oryzae | 1 | species | plants | fungi | 661394 |
| trichuris vulpis | 20 | species | invertebrates | helminths | 219738 |
| trichuris trichiura | 51 | species | invertebrates | helminths | 36087 |
| trichuris suis | 27 | species | invertebrates | helminths | 68888 |
| trichostrongylus vitrinus | 19 | species | invertebrates | helminths | 40352 |
| trichostrongylus skrjabini | -3 | species | | helminths | |
| trichostrongylus probolurus | 3 | species | invertebrates | helminths | 53330 |
| trichostrongylus orientalis | 1 | species | | helminths | |
| trichostrongylus lerouxi | 1 | species | | helminths | |
| trichostrongylus instabilis | -3 | species | | helminths | |
| trichostrongylus colubriformis | 57 | species | invertebrates | helminths | 6319 |
| trichostrongylus capricola | 3 | species | invertebrates | helminths | 126400 |
| trichostrongylus calcaratus | 2 | species | | helminths | |
| trichostrongylus brevis | -3 | species | | helminths | |
| trichostrongylus axei | 22 | species | invertebrates | helminths | 40349 |
| trichostrongylus affinis | 2 | species | | helminths | |
| trichosporon ovoides | 4 | species | plants | fungi | 82524 |
| trichosporon inkin | 9 | species | plants | fungi | 82517 |
| trichosporon beigelii | 40 | species | plants | fungi | 5553 |
| trichosporon asahii | 20 | species | plants | fungi | 82508 |
| trichophyton violaceum | 23 | species | plants | fungi | 34388 |
| trichophyton verrucosum | 19 | species | plants | fungi | 63417 |
| trichophyton tonsurans | 34 | species | plants | fungi | 34387 |
| trichophyton soudanense | 13 | species | plants | fungi | 69891 |
| trichophyton schoenleinii | 12 | species | plants | fungi | 34386 |
| trichophyton rubrum | 48 | species | plants | fungi | 5551 |
| trichophyton mentagrophytes | 41 | species | plants | fungi | 523103 |
| trichophyton gourvilii | 1 | species | plants | fungi | 81477 |
| trichophyton equinum | 10 | species | plants | fungi | 63418 |
| trichophyton concentricum | 5 | species | plants | fungi | 63419 |
| trichomonas vaginalis | 87 | species | invertebrates | protozoa | 5722 |
| trichomonas tenax | 11 | species | invertebrates | protozoa | 43075 |
| trichomaris invadens | 4 | species | | fungi | |
| trichoderma viride | 64 | species | plants | fungi | 5547 |
| trichoderma pseudokoningii | 15 | species | plants | fungi | 317029 |
| trichobilharzia stagnicolae | 3 | species | invertebrates | helminths | 596254 |
| trichobilharzia ocellata | 30 | species | invertebrates | helminths | 100602 |