| dengue virus | 99 | species | viruses | viruses | 12637 |
| delftia acidovorans | 40 | species | bacteria | bacteria | 80866 |
| dakar bat virus | 1 | species | viruses | viruses | 64282 |
| cystoisospora belli | 32 | species | invertebrates | protozoa | 482538 |
| cystobasidium minutum | 16 | species | plants | fungi | 29899 |
| cyphellophora suttonii | -3 | species | plants | fungi | 856651 |
| cylindrocarpon vaginae | -3 | species | | fungi | |
| cylindrocarpon cyanescens | 1 | species | | fungi | |
| cyclospora cayetanensis | 30 | species | invertebrates | protozoa | 88456 |
| cyclodontostomum purvisi | 2 | species | invertebrates | helminths | 321341 |
| cutaneotrichosporon mucoides | 10 | species | plants | fungi | 82522 |
| cutaneotrichosporon cutaneum | 38 | species | plants | fungi | 5554 |
| curvularia verruculosa | 2 | species | plants | fungi | 95740 |
| curvularia senegalensis | 4 | species | plants | fungi | 215132 |
| curvularia pallescens | 7 | no rank | plants | fungi | 491261 |
| curvularia lunata | 34 | species | plants | fungi | 5503 |
| curvularia hawaiiensis | 12 | species | plants | fungi | 1230527 |
| curvularia clavata | 3 | species | plants | fungi | 95742 |
| curvularia brachyspora | 4 | species | plants | fungi | 39400 |
| curvularia australiensis | 6 | species | plants | fungi | 91365 |
| cunninghamella bertholletiae | 25 | species | plants | fungi | 90251 |
| cryptosporidium parvum | 92 | species | invertebrates | protozoa | 5807 |
| cryptocotyle lingua | 21 | species | invertebrates | helminths | 66766 |
| cryptococcus neoformans | 126 | species | plants | fungi | 5207 |
| cronobacter sakazakii | 43 | species | bacteria | bacteria | 28141 |
| coxiella burnetii | 67 | species | bacteria | bacteria | 777 |
| cowpox virus | 71 | species | viruses | viruses | 10243 |
| corynosoma strumosum | 7 | species | invertebrates | helminths | 141827 |
| corynebacterium xerosis | 21 | species | bacteria | bacteria | 1725 |
| corynebacterium urealyticum | 15 | species | bacteria | bacteria | 43771 |
| corynebacterium ulcerans | 18 | species | bacteria | bacteria | 65058 |
| corynebacterium striatum | 19 | species | bacteria | bacteria | 43770 |
| corynebacterium pseudotuberculosis | 33 | species | bacteria | bacteria | 1719 |
| corynebacterium pseudodiphtheriticum | 13 | species | bacteria | bacteria | 37637 |
| corynebacterium propinquum | 5 | species | bacteria | bacteria | 43769 |
| corynebacterium minutissimum | 16 | species | bacteria | bacteria | 38301 |
| corynebacterium macginleyi | 7 | species | bacteria | bacteria | 38290 |
| corynebacterium kutscheri | 11 | species | bacteria | bacteria | 35755 |
| corynebacterium jeikeium | 22 | species | bacteria | bacteria | 38289 |
| corynebacterium diphtheriae | 64 | species | bacteria | bacteria | 1717 |
| corynebacterium bovis | 27 | species | bacteria | bacteria | 36808 |
| corynebacterium argentoratense | 3 | species | bacteria | bacteria | 42817 |
| corynebacterium afermentans | 10 | species | bacteria | bacteria | 38286 |
| coprinopsis cinerea | 61 | species | plants | fungi | 5346 |
| contracaecum osculatum | 19 | species | invertebrates | helminths | 106324 |
| coniochaeta mutabilis | 5 | species | plants | fungi | 177207 |
| coniochaeta hoffmannii | 4 | species | plants | fungi | 91930 |
| conidiobolus lamprauges | 5 | species | plants | fungi | 90250 |
| conidiobolus incongruus | 7 | species | plants | fungi | 90249 |
| conidiobolus coronatus | 19 | species | plants | fungi | 34488 |
| comamonas testosteroni | 50 | species | bacteria | bacteria | 285 |
| colorado tick fever virus | 17 | species | viruses | viruses | 46839 |
| collinsella aerofaciens | 19 | species | bacteria | bacteria | 74426 |
| colletotrichum gloeosporioides | 48 | species | plants | fungi | 474922 |
| colletotrichum dematium | 13 | species | plants | fungi | 34405 |
| colletotrichum coccodes | 24 | species | plants | fungi | 27358 |
| cokeromyces recurvatus | 7 | species | plants | fungi | 90255 |
| coccidioides immitis | 54 | species | plants | fungi | 5501 |
| clostridium tetani | 26 | species | bacteria | bacteria | 1513 |
| clostridium tertium | 17 | species | bacteria | bacteria | 1559 |
| clostridium sporogenes | 33 | species | bacteria | bacteria | 1509 |
| clostridium septicum | 31 | species | bacteria | bacteria | 1504 |
| clostridium perfringens | 101 | species | bacteria | bacteria | 1502 |
| clostridium novyi | 25 | species | bacteria | bacteria | 1542 |
| clostridium moniliforme | 1 | species | bacteria | bacteria | 39489 |
| clostridium fallax | 5 | species | bacteria | bacteria | 1533 |
| clostridium chauvoei | 15 | species | bacteria | bacteria | 46867 |
| clostridium butyricum | 53 | species | bacteria | bacteria | 1492 |
| clostridium botulinum | 106 | species | bacteria | bacteria | 1491 |
| clostridium baratii | 16 | species | bacteria | bacteria | 1561 |
| clostridioides difficile | 127 | species | bacteria | bacteria | 1496 |
| clinostomum complanatum | 6 | species | invertebrates | helminths | 235145 |
| clavispora lusitaniae | 40 | species | plants | fungi | 36911 |
| cladosporium sphaerospermum | 18 | species | plants | fungi | 92950 |
| cladosporium oxysporum | 8 | species | plants | fungi | 29919 |
| cladosporium cladosporioides | 29 | species | plants | fungi | 29917 |
| cladorrhinum bulbillosum | 1 | species | plants | fungi | 585595 |
| cladophialophora devriesii | 1 | species | plants | fungi | 82107 |
| cladophialophora carrionii | 15 | species | plants | fungi | 86049 |
| cladophialophora boppii | 2 | species | plants | fungi | 82106 |
| cladophialophora bantiana | 21 | species | plants | fungi | 89940 |
| cladophialophora arxii | 2 | species | plants | fungi | 82108 |
| citrobacter youngae | 5 | species | bacteria | bacteria | 133448 |
| citrobacter werkmanii | 4 | species | bacteria | bacteria | 67827 |
| citrobacter sedlakii | 6 | species | bacteria | bacteria | 67826 |
| citrobacter rodentium | 45 | species | bacteria | bacteria | 67825 |
| citrobacter koseri | 31 | species | bacteria | bacteria | 545 |
| citrobacter freundii | 70 | species | bacteria | bacteria | 546 |
| citrobacter farmeri | 4 | species | bacteria | bacteria | 67824 |
| citrobacter braakii | 10 | species | bacteria | bacteria | 57706 |
| citrobacter amalonaticus | 12 | species | bacteria | bacteria | 35703 |
| chryseobacterium balustinum | 10 | species | bacteria | bacteria | 246 |
| chromobacterium violaceum | 53 | species | bacteria | bacteria | 536 |
| chlamydoabsidia padenii | -3 | species | plants | fungi | 90267 |
| chlamydia trachomatis | 129 | species | bacteria | bacteria | 813 |
| chlamydia psittaci | 63 | species | bacteria | bacteria | 83554 |
| chlamydia pneumoniae | 143 | species | bacteria | bacteria | 83558 |
| chikungunya virus | 39 | species | viruses | viruses | 37124 |
| cheilospirura | 5 | genus | | | |
| changuinola virus | -3 | species | | viruses | 40052 |