The North Pontic region, which encompasses present-day Ukraine, was a crossroads of migration, connecting the vast Eurasian Steppe with Central Europe. We generated shotgun-sequenced genomic data for 91 individuals dating from around 7000 BCE to 1800 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. We infer a high degree of temporal heterogeneity in ancestry, with fluctuating genetic affinities to different present-day Eurasian 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. In short, our study reveals a diverse range of ancestries in the Ukraine region through time as a result of frequent movements, assimilation, and contacts.