The paper focuses on the results of diatoms analysis of the bottom sediments from the New and Ancient Azov layers from the cores, sampled in various areas of the Sea of Azov. To analyze the specific features of change of floristic complexes of diatoms in bottom sediments, we focused on the detailed description of species composition from three cores: Tz-VII (Central Taganrog Bay), St-1 (central part of the Sea) and K-59.19 (the southern part of the Sea). These three cores are the most indicative as they contain sediments from both the Ancient and New Azov layers. The implemented studies allowed comparing the diatoms flora, existing during the Middle and Late Holocene in the open part of the Sea of Azov and in the Taganrog Bay (water area). As a result of deposits’ analysis, the age of which is from the recent period to 6.5 thousand years ago, 87 taxa of diatoms, as well as the resting spores of dinoflagellates and stomatocysts of golden algae were registered. The results of diatoms analysis indicate rather a distinct correlation of changes in species composition of microalgae with the water level fluctuations in the reservoir.