| Udeniomyces megalosporus | NBRC 10754T |
| Udeniomyces puniceus | NBRC 1337T |
| Udeniomyces pyricola | NBRC 10115, NBRC 10116T |
| Uliginosibacterium aquaticum | NBRC 114418T |
| Uliginosibacterium gangwonense | NBRC 106428T |
| Uliginosibacterium sp. | NBRC 116067, NBRC 116068 |
| Ulkenia amoeboidea | NBRC 104106 |
| Ulkenia sp. | NBRC 110830, NBRC 110831, NBRC 110832, NBRC 111917 |
| Ulocladium botrytis | NBRC 9210, NBRC 32273 |
| Ulocladium consortiale | NBRC 8823, NBRC 8824 |
| Ulvibacter antarcticus | NBRC 102682T |
| Ulvibacter marinus | NBRC 109484T |
| Umbelopsis angularis | NBRC 5426, NBRC 6744, NBRC 8186, NBRC 8187 |
| Umbelopsis gibberispora | NBRC 107819 |
| Umbelopsis isabellina | NBRC 6336, NBRC 6739, NBRC 7824, NBRC 7873T, NBRC 7874, NBRC 7884, NBRC 8183, NBRC 8286, NBRC 8308, NBRC 8309, NBRC 8572, NBRC 105998, NBRC 110180 |
| Umbelopsis nana | NBRC 8190, NBRC 8794, NBRC 100664, NBRC 102295, NBRC 105995, NBRC 117090 |
| Umbelopsis ramanniana | NBRC 7825, NBRC 8184, NBRC 8185, NBRC 8287, NBRC 102500, NBRC 102501, NBRC 102502, NBRC 105996, NBRC 107816 |
| Umbelopsis roseonana | NBRC 102314 |
| Umbelopsis vinacea | NBRC 6738, NBRC 7875, NBRC 100665, NBRC 105997 |
| Umboniibacter caenipelagi | NBRC 112760T |
| Umezawaea tangerina | NBRC 16184T |
| Uncinocarpus reesii | NBRC 32079, NBRC 100320 |
| Undibacterium jejuense | NBRC 108922T |
| Undibacterium seohonense | NBRC 108929T |
| Undibacterium terreum | NBRC 108789T |
| Unguispora rhaphidophoridarum | NBRC 114905, NBRC 114906T, NBRC 114907 |
| unicelluar-cyanophyte (Class: Cyanophyceae) | NBRC 115805 |
| unicellular-rhodophyte (Class: Rhodellophyceae) | NBRC 102937, NBRC 102938, NBRC 102939 |
| unicellular-rhodophyte (Class: Stylonematophyceae) | NBRC 102723 |
| unicellular-ulvophyte (Class: Ulvophyceae) | NBRC 102767, NBRC 102779, NBRC 102780, NBRC 102783, NBRC 102828, NBRC 102836, NBRC 102900, NBRC 102901 |
| Urceolella carestiana | NBRC 108588 |
| Ureibacillus composti | NBRC 106533T |
| Ureibacillus suwonensis | NBRC 106534T |
| Ureibacillus thermophilus | NBRC 106535T |
| Ureibacillus thermosphaericus | NBRC 108682 |
| Urnula craterium | NBRC 30137, NBRC 31627 |
| Urocystis agropyri | NBRC 32750, NBRC 32751 |
| Uronema sp. (class: Chlorophyceae) | NBRC 113204 |
| Uruburuella sp. | NBRC 113501 |
| Ustilaginoidea virens | NBRC 5923, NBRC 9175, NBRC 31672, NBRC 31673 |
| Ustilago coicis | NBRC 32733, NBRC 32734 |
| Ustilago crus-galli | NBRC 31947, NBRC 32737, NBRC 32738 |
| Ustilago cynodontis | NBRC 7530, NBRC 9727, NBRC 9758, NBRC 115026 |
| Ustilago esculenta | NBRC 9887, NBRC 105094, NBRC 105096, NBRC 105097, NBRC 105098 |
| Ustilago kusanoi | NBRC 9070 |
| Ustilago maydis | NBRC 5346, NBRC 6907 |
| Ustilago neglecta | NBRC 32748, NBRC 32749 |
| Ustilago onumae | NBRC 9071 |
| Ustilago phragmitis | NBRC 115016 |
| Ustilago rabenhorstiana | NBRC 8995 |
| Ustilago scitaminea | NBRC 32729, NBRC 32730 |
| Ustilago shiraiana | NBRC 8809, NBRC 30149 |
| Ustilago sphaerogena | NBRC 31946, NBRC 32735, NBRC 32736 |
| Ustilago syntherismae | NBRC 32724, NBRC 32725, NBRC 32726 |
| Ustilago trichophora | NBRC 100155, NBRC 100156, NBRC 100157, NBRC 100158, NBRC 100159, NBRC 100160 |
| Ustilago utriculosa | NBRC 32739, NBRC 32740 |
| Ustilago violacea | NBRC 9216, NBRC 9218, NBRC 30031 |
| Uthatobasidium fusisporum | NBRC 6281 |
