Diverse microbial communities in the Black Sea respond differently to environmental changes. The Black Sea has a distinct ecosystem with a thin layer of oxic-zone above and anoxic-zone below. The Black Sea microbiota has been investigated using high-throughput genomic studies, but there are no studies on seasonal and vertical fluctuations in microbial community composition, driving force, or community assembly mechanisms. Next Generation Sequencing targeting the hypervariable V3 and V4 regions of the 16S rRNA gene was used to examine the diversity, abundance, and community structure of seasonal, vertical, and horizontal microbial communities. 750 bacterial and three archaeal species from 25 different phyla were assigned to the detected OTUs. From the surface to deeper zones, the number of OTUs and the diversity of organisms increased. Similar microbial community compositions were observed at each sampling station. However, the composition of microbial communities differed dramatically vertically between zones. The community composition of seawater and sediment also differed significantly. Summer composition differed significantly from other seasons at 5 meters, while the remaining depths appeared similar. For the first time in the Black Sea, nitrite-oxidizing (Nitrosospira tenuis, N. multiformis, Nitrospira rev-210106-rev lenta), sulfate-reducing (Thermodesulfovibrio hydrogeniphilus), thiosulfate-reducing (Shewanella hafniensis, S. vesiculosa), iron-reducing (Geoalkalibacter ferrihydriticus), Fe-Mn reducing (Geoalkalibacter subterraneus) and electricity-producing (Geobacter sulfurreducens) bacteria were reported. Proteobacteria dominated all the sampling depths. The abundance of Cyanobacteria was highest in the surface mixed zone. Proteobacteria, Cyanobacteria, Bacteroidetes, and Verrucomicrobia were found across the whole water column, but Nitrospinae, Chloroflexi, and Kiritimatiellaeota were limited to depths of 75 meters or deeper, where they were prevalent. Variation in the vertical composition of microbial communities is caused by environmental conditions and their responses to different ecological niches. Acknowledgment. This work study was supported by the Scientific and Technological Research Council of Turkey (grant number 117Y381).