| Udeniomyces megalosporus | 10754T |
| Udeniomyces puniceus | 1337T |
| Udeniomyces pyricola | 10115, 10116T |
| Uliginosibacterium gangwonense | 106428T |
| Uliginosibacterium sp. | 116067, 116068 |
| Ulkenia amoeboidea | 104106 |
| Ulkenia sp. | 110830, 110831, 110832, 111917 |
| Ulocladium botrytis | 9210, 32273 |
| Ulocladium consortiale | 8823, 8824 |
| Ulvibacter antarcticus | 102682T |
| Ulvibacter marinus | 109484T |
| Umbelopsis angularis | 5426, 6744, 8186, 8187 |
| Umbelopsis gibberispora | 107819 |
| Umbelopsis isabellina | 6336, 6739, 7824, 7873T, 7874, 7884, 8183, 8286, 8308, 8309, 8572, 105998, 110180 |
| Umbelopsis nana | 8190, 8794, 100664, 102295, 105995 |
| Umbelopsis ramanniana | 7825, 8184, 8185, 8287, 102500, 102501, 102502, 105996, 107816 |
| Umbelopsis roseonana | 102314 |
| Umbelopsis vinacea | 6738, 7875, 100665, 105997 |
| Umboniibacter caenipelagi | 112760T |
| Umezawaea tangerina | 16184T |
| Uncinocarpus reesii | 32079, 100320 |
| Undibacterium jejuense | 108922T |
| Undibacterium seohonense | 108929T |
| Undibacterium terreum | 108789T |
| Unguispora rhaphidophoridarum | 114905, 114906T, 114907 |
| unicelluar-cyanophyte (Class: Cyanophyceae) | 115805 |
| unicellular-rhodophyte (Class: Rhodellophyceae) | 102937, 102938, 102939 |
| unicellular-rhodophyte (Class: Stylonematophyceae) | 102723 |
| unicellular-ulvophyte (Class: Ulvophyceae) | 102767, 102779, 102780, 102783, 102828, 102836, 102900, 102901 |
| Urceolella carestiana | 108588 |
| Ureibacillus composti | 106533T |
| Ureibacillus suwonensis | 106534T |
| Ureibacillus thermophilus | 106535T |
| Ureibacillus thermosphaericus | 108682 |
| Urnula craterium | 30137, 31627 |
| Urocystis agropyri | 32750, 32751 |
| Uronema sp. (class: Chlorophyceae) | 113204 |
| Uruburuella sp. | 113501 |
| Ustilaginoidea virens | 5923, 9175, 31672, 31673 |
| Ustilago coicis | 32733, 32734 |
| Ustilago crus-galli | 31947, 32737, 32738 |
| Ustilago cynodontis | 7530, 9727, 9758, 115026 |
| Ustilago esculenta | 9887, 105094, 105096, 105097, 105098 |
| Ustilago kusanoi | 9070 |
| Ustilago maydis | 5346, 6907 |
| Ustilago neglecta | 32748, 32749 |
| Ustilago onumae | 9071 |
| Ustilago phragmitis | 115016 |
| Ustilago rabenhorstiana | 8995 |
| Ustilago scitaminea | 32729, 32730 |
| Ustilago shiraiana | 8809, 30149 |
| Ustilago sphaerogena | 31946, 32735, 32736 |
| Ustilago syntherismae | 32724, 32725, 32726 |
| Ustilago trichophora | 100155, 100156, 100157, 100158, 100159, 100160 |
| Ustilago utriculosa | 32739, 32740 |
| Ustilago violacea | 9216, 9218, 30031 |
| Uthatobasidium fusisporum | 6281 |
