The North Pontic region, which encompasses present-day Ukraine, was a crossroads of migration as it connected the vast Eurasian Steppe with Central Europe. We generated shotgun-sequenced genomic data for 91 individuals dating from around 7,000 BCE to 1,800 CE to study migration and mobility history in the region, with a particular focus on historically attested migrating groups during the Iron Age and the medieval period, such as Scythian, Chernyakhiv, Saltiv and Nogai associated peoples. We infer a high degree of temporal heterogeneity in ancestry, with fluctuating genetic affinities to present-day Western European, Eastern European, Western Steppe and East Asian groups. We also infer high heterogeneity in ancestry within geographically, culturally and socially defined groups. Despite this, we find that ancestry components which are widespread in Eastern and Central Europe have been present in the Ukraine region since the Bronze Age.