© 2019 Collegium Boreas. Published by John Wiley & Sons Ltd The study presents the first description and analysis of ostracod records from three sites cored in different parts of the Baltic Sea during the IODP Expedition 347, Baltic Sea Paleoenvironment. Our data present the first high-resolution ostracod records from the Late Weichselian and Holocene sediments collected across the Baltic Sea Basin. Using published data on modern ostracod species ecology of the Baltic Sea, we were able to provide ostracod-based palaeoreconstructions of the history of the region. The stratigraphical framework for the sites is based on radiocarbon-based age models. The three studied sites reveal different ostracod assemblage successions that reflect environmental changes in the study area. Site M0060, located in the Kattegat area, contains the oldest ostracod assemblages that document a marine environment with very high sedimentation rates during the most recent deglaciation. Between ~13 000 and 7500 cal. a BP a modern-like near-shore environment developed. Site M0059 in the southwestern Baltic Sea, Little Belt area, contains assemblages reflecting the transition from a freshwater lake to the brackish Littorina Sea between ~7500 and 7300 cal. a BP. Site M0063 is the deepest location in the central Baltic, Landsort Deep, and yielded very limited ostracod data, but comparison with our organic carbon data allowed us to distinguish the Yoldia Sea, Ancylus Lake and Littorina Sea intervals. The ostracod record correlates well with the organic carbon record with alternation between periods of hypoxia and periods of low oxygen that still supported ostracods.