| chapare mammarenavirus | 2 | species | viruses | viruses | 499556 |
| cheilospirura | 5 | genus | | | |
| cheilospirura hamulosa | 3 | species | | helminths | |
| cheyletiella blakei | 5 | species | | | |
| cheyletiella furmani | -3 | species | | | |
| cheyletiella parasitivorax | 9 | species | | | |
| cheyletiella strandtmanni | -3 | species | | | |
| cheyletiella yasguri | 9 | species | | | |
| chick syncytial virus | 3 | species | viruses | viruses | 353768 |
| chicken anemia virus | 60 | species | viruses | viruses | 12618 |
| chikungunya virus | 39 | species | viruses | viruses | 37124 |
| chilodonella cyprini | 4 | species | invertebrates | protozoa | 639309 |
| chirodiscoides caviae | 3 | species | | | |
| chlamydia | 178 | genus | bacteria | | 810 |
| chlamydia abortus | 63 | species | bacteria | bacteria | 83555 |
| chlamydia caviae | 9 | species | bacteria | bacteria | 83557 |
| chlamydia felis | 17 | species | bacteria | bacteria | 83556 |
| chlamydia pecorum | 21 | species | bacteria | bacteria | 85991 |
| chlamydia pneumoniae | 143 | species | bacteria | bacteria | 83558 |
| chlamydia psittaci | 63 | species | bacteria | bacteria | 83554 |
| chlamydia trachomatis | 129 | species | bacteria | bacteria | 813 |
| chlamydoabsidia padenii | -3 | species | plants | fungi | 90267 |
| chlamydophila | 35 | genus | bacteria | | 83553 |
| choanotaenia infundibulum | 7 | species | invertebrates | helminths | 227339 |
| choriopsoroptes kenyensis | 1 | species | | | |
| chorioptes bovis | 10 | species | invertebrates | | 420257 |
| chorioptes texanus | 5 | species | invertebrates | | 411904 |
| chromobacterium | 64 | genus | bacteria | | 535 |
| chromobacterium violaceum | 53 | species | bacteria | bacteria | 536 |
| chronic wasting disease | 49 | | | | |
| chryseobacterium | 31 | genus | bacteria | | 59732 |
| chryseobacterium balustinum | 10 | species | bacteria | bacteria | 246 |
| chrysomya bezziana | 14 | species | invertebrates | fly | 69364 |
| chrysomya chloropyga | 6 | species | invertebrates | fly | 142978 |
| chrysomya megacephala | 16 | species | invertebrates | fly | 115424 |
| chrysomya micropogon | -3 | species | | fly | |
| chrysomya rufifacies | 20 | species | invertebrates | fly | 45450 |
| chrysomya varipes | 2 | species | invertebrates | fly | 142905 |
| cimex lectularius | 27 | species | invertebrates | | 79782 |
| circoviridae ng24 | -3 | species | viruses | viruses | 745094 |
| circovirus | 68 | genus | viruses | | 39725 |
| citrobacter | 83 | genus | bacteria | | 544 |
| citrobacter amalonaticus | 12 | species | bacteria | bacteria | 35703 |
| citrobacter braakii | 10 | species | bacteria | bacteria | 57706 |
| citrobacter farmeri | 4 | species | bacteria | bacteria | 67824 |
| citrobacter freundii | 70 | species | bacteria | bacteria | 546 |
| citrobacter koseri | 31 | species | bacteria | bacteria | 545 |
| citrobacter rodentium | 45 | species | bacteria | bacteria | 67825 |
| citrobacter sedlakii | 6 | species | bacteria | bacteria | 67826 |
| citrobacter werkmanii | 4 | species | bacteria | bacteria | 67827 |
| citrobacter youngae | 5 | species | bacteria | bacteria | 133448 |
| cittotaenia ctenoides | -3 | species | | helminths | |
| cittotaenia denticulata | 3 | species | | helminths | |
| cittotaenia pectinata | 1 | species | | helminths | |
| cladophialophora arxii | 2 | species | plants | fungi | 82108 |
| cladophialophora bantiana | 21 | species | plants | fungi | 89940 |
| cladophialophora boppii | 2 | species | plants | fungi | 82106 |
| cladophialophora carrionii | 15 | species | plants | fungi | 86049 |
| cladophialophora devriesii | 1 | species | plants | fungi | 82107 |
| cladorrhinum bulbillosum | 1 | species | plants | fungi | 585595 |
| cladosporium cladosporioides | 29 | species | plants | fungi | 29917 |
| cladosporium oxysporum | 8 | species | plants | fungi | 29919 |
| cladosporium sphaerospermum | 18 | species | plants | fungi | 92950 |
| classical swine fever virus | 84 | species | viruses | viruses | 11096 |
| clavibacter | 39 | genus | bacteria | | 1573 |
| clavispora lusitaniae | 40 | species | plants | fungi | 36911 |
| clinostomum complanatum | 6 | species | invertebrates | helminths | 235145 |
| clinostomum marginatum | 8 | species | invertebrates | helminths | 234884 |
| clonorchis sinensis | 30 | species | invertebrates | helminths | 79923 |
| clostridioides difficile | 127 | species | bacteria | bacteria | 1496 |
| clostridioides difficile cip 107932 | -3 | no rank | bacteria | bacteria | 499176 |
| clostridium | 198 | genus | bacteria | | 1485 |
| clostridium baratii | 16 | species | bacteria | bacteria | 1561 |
| clostridium botulinum | 106 | species | bacteria | bacteria | 1491 |
| clostridium butyricum | 53 | species | bacteria | bacteria | 1492 |
| clostridium chauvoei | 15 | species | bacteria | bacteria | 46867 |
| clostridium fallax | 5 | species | bacteria | bacteria | 1533 |
| clostridium haemolyticum | 5 | species | bacteria | bacteria | 84025 |
| clostridium moniliforme | 1 | species | bacteria | bacteria | 39489 |
| clostridium novyi | 25 | species | bacteria | bacteria | 1542 |
| clostridium perfringens | 101 | species | bacteria | bacteria | 1502 |
| clostridium perfringens b | 3 | no rank | bacteria | bacteria | 451751 |
| clostridium septicum | 31 | species | bacteria | bacteria | 1504 |
| clostridium sporogenes | 33 | species | bacteria | bacteria | 1509 |
| clostridium tertium | 17 | species | bacteria | bacteria | 1559 |
| clostridium tetani | 26 | species | bacteria | bacteria | 1513 |
| cnemidocoptes gallinae | 1 | species | | | |
| cnemidocoptes jamaicensis | 1 | species | | | |
| cnemidocoptes mutans | 1 | species | | | |
| cnemidocoptes pilae | 1 | species | | | |
| coccidioides immitis | 54 | species | plants | fungi | 5501 |
| coccidioides posadasii | 14 | species | plants | fungi | 199306 |
| cochliomyia hominivorax | 24 | species | invertebrates | fly | 115425 |
| cochliomyia macellaria | 16 | species | invertebrates | fly | 66361 |
| codiostomum struthionis | 2 | species | | helminths | |
| coenonia | 2 | genus | bacteria | | 78328 |
| cokeromyces recurvatus | 7 | species | plants | fungi | 90255 |
| colletotrichum coccodes | 24 | species | plants | fungi | 27358 |
| colletotrichum dematium | 13 | species | plants | fungi | 34405 |
| colletotrichum gloeosporioides | 48 | species | plants | fungi | 474922 |