| Zalerion maritima | 8619, 32164 |
| Zalerion xylestrix | 7836 |
| Zancudomyces culisetae | 111172, 111173 |
| Zarea aleophila | 31179 |
| Zeaxanthinibacter enoshimensis | 101990T |
| Zhihengliuella aestuarii | 109060T |
| Zhihengliuella alba | 109061T |
| Zhihengliuella flava | 109021T |
| Zhihengliuella halotolerans | 107838T |
| Zhihengliuella salsuginis | 109062T |
| Zhongshania ponticola | 113193 |
| Zimmermannella alba | 15616T |
| Zobellia uliginosa | 14962T |
| Zoogloea oryzae | 102407T |
| Zoogloea ramigera | 15342T |
| Zopfiella erostrata | 109852 |
| Zopfiella karachiensis | 32902, 32903 |
| Zopfiella latipes | 9826, 30408, 30409 |
| Zopfiella leucotricha | 9828, 31819, 32848 |
| Zopfiella lundqvistii | 30585T, 30643, 30644, 30645, 30646, 30647, 30648, 30649, 30650, 30651, 30652 |
| Zopfiella marina | 30420T |
| Zopfiella matsushimae | 30217T |
| Zopfiella pilifera | 9558T |
| Zwartia vadi | 114902T |
| Zygoascus hellenicus | 1575T, 10183, 10184T, 10185, 10186, 10187, 10246, 10720 |
| Zygophiala jamaicensis | 31255, 31256, 31257, 31258, 31259, 31260, 31261, 31262, 31263, 31264, 31265, 31266, 31267, 31268, 31269, 31270, 31271, 31272, 31273, 31274, 31275, 31276, 31277 |
| Zygorhynchus californiensis | 6663T |
| Zygorhynchus exponens var. exponens | 6664T, 100515, 100517, 100518 |
| Zygorhynchus exponens var. smithii | 6665T |
| Zygorhynchus moelleri | 4832, 4833, 5305, 100516, 105999 |
| Zygosaccharomyces bailii | 0468, 0493, 0519, 1098T, 1137, 1611, 1801, 10667 |
| Zygosaccharomyces bisporus | 0467, 0723, 1131T, 1249, 1250, 1734, 1736, 1737 |
| Zygosaccharomyces kombuchaensis | 112840T |
| Zygosaccharomyces lentus | 111512T |
| Zygosaccharomyces mellis | 0485, 1055, 1615T, 1732, 101874, 101875, 101876 |
| Zygosaccharomyces parabailii | 1047T |
| Zygosaccharomyces pseudobailii | 0488T |
| Zygosaccharomyces rouxii | 0487, 0489, 0494, 0495, 0510, 0511, 0512, 0513, 0533, 0597, 0686, 0740, 0846, 1053, 1130T, 1252, 1730, 1733, 1813, 1814, 1877, 1914, 1960, 10652, 10653, 10654, 10655, 10656, 10657, 10658, 10659, 10660, 10669, 10670, 10671, 110957 |
| Zygosaccharomyces siamensis | 116063 |
| Zygosaccharomyces sp. | 0320, 0439, 0505, 0506, 0517, 0521, 0523, 0525, 0596, 0845, 1778, 1780, 1812, 1876, 1945, 10668, 10672, 11069, 11070, 11071, 105675, 105676, 115917 |
| Zygosporium gibbum | 30213 |
| Zygosporium masonii | 30214 |
| Zygosporium mycophilum | 9359, 32050 |
| Zygotorulaspora florentinus | 1088T, 1806, 1807, 1808, 1809, 1810, 1993, 11088 |
| Zygotorulaspora mrakii | 1835T |
| Zygozyma arxii | 10914T |
| Zygozyma oligophaga | 10360T |
| Zygozyma suomiensis | 10920T |
| Zymobacter palmae | 102412T |
| Zymomonas mobilis subsp. mobilis | 13756 |
| Zymomonas mobilis subsp. pomaceae | 13757T |
