We present the first comprehensive taxonomic and environmental study of dinoflagellate cysts in 185 surface sediment samples from the Black Sea Corridor (BSC) which is a series of marine basins extending from the Aegean to the Aral Seas (including Marmara, Black, Azov and Caspian Seas). For decades, these low-salinity, semi-enclosed or endorheic basins have experienced large-scale changes because of intensive agriculture and industrialisation, with consequent eutrophication and increased algal blooms. The BSC atlas data provide a baseline for improved understanding of linkages between surface water conditions and dinoflagellate cyst (dinocyst) distribution, diversity and morphological variations. By cross-reference to dinocyst occurrences in sediment cores with radiocarbon ages covering the past c. 11,700 years, the history of recent biodiversity changes can be evaluated. The seabed cyst samples integrate seasonal and multi-year data which are not usually captured by plankton samples, and the cyst composition can point to presence of previously unrecorded motile dinoflagellate species in the BSC. Results show the presence of at least 71 dinocyst taxa of which 36% can be related to motile stages recorded in the plankton. Comparison with sediment core records shows that five new taxa appear to have entered or re-entered the region over the past century. Statistical analysis of the atlas data reveals the presence of four ecological assemblages which are primarily correlated with seasonal and annual surface water salinity and temperature; correlation with phosphate, nitrate and silicate nutrients, chlorophyll-a and bottom water oxygen is less clear but may be important for some taxa. Biodiversity indices reveal strong west − east biogeographical differences among the basins that reflect the different histories of Mediterranean versus Ponto-Caspian connections. The atlas data provide a standardised taxonomy and regional database for interpreting downcore cyst variations in terms of quantitative oceanographic changes. The atlas also provides a baseline for monitoring further changes in the BSC dinocysts that may accompany the accelerating development of the region.