The geographic distribution, level of taxonomic diversity, and ecological preferences of Bacillariophyta complexes extracted from Paleogene deposits in various regions of Ukraine are characterized. The stratigraphic sequence of diatom assemblages, the relationship of the conditions of their formation to paleoceanological events in sedimentation basins, and the biostratigraphic significance are traced. The most taxonomically diverse (up to 250 species) associations of marine diatoms and silicoflagellates are found in the Middle to Upper Eocene deposits of the northeast margin of the Dnieper-Donetsk Depression, the northwest margins of the Donbas, and the slopes of the Voronezh Uplift. In Eocene-Oligocene deposits of the Ukrainian Shield, diatom complexes consist of over 60 marine and brackish taxa. Early Oligocene marine associations, widespread in the Sambir Carpathians and the eastern part of the Azov region, include over 130 species-level taxa. Changes in the proportion of ecological groups of diatom algae indicate their formation under different facies conditions and the transition from marine warm to more cold-water coastal-marine environments during the Eocene, with episodes of freshwater input in the Oligocene.