Archaeological consideration of maritime connectivity has ranged from a biogeographical perspective that considers the sea as a barrier to a view of seaways as ancient highways that facilitate exchange. Our results illustrate the former. We report three Late Neolithic human genomes from the Mediterranean island of Malta that are markedly enriched for runs of homozygosity, indicating inbreeding in their ancestry and an effective population size of only hundreds, a striking illustration of maritime isolation in this agricultural society. In the Late Neolithic, communities across mainland Europe experienced a resurgence of hunter-gatherer ancestry, pointing toward the persistence of different ancestral strands that subsequently admixed. This is absent in the Maltese genomes, giving a further indication of their genomic insularity. Imputation of genome-wide genotypes in our new and 258 published ancient individuals allowed shared identity-by-descent segment analysis, giving a fine-grained genetic geography of Neolithic Europe. This highlights the differentiating effects of seafaring Mediterranean expansion and also island colonization, including that of Ireland, Britain, and Orkney. These maritime effects contrast profoundly with a lack of migratory barriers in the establishment of Central European farming populations from Anatolia and the Balkans. [Display omitted] • Three inbred genomes from Malta, dated around 2500 BC • As in moderns, the genetic structure of Neolithic genomes is shaped by geography • Genomic insularity of island Neolithic populations • A marked distinction between the Danubian and Mediterranean farming expansion routes Using high-coverage genomes from ancient Maltese, Ariano et al. show that they had signals of both recent and more distant inbreeding, indicating small population size. Using diploid genome-wide data, the authors explore the genetic geography of Neolithic Europe which, echoing modern patterns, is shaped by physical topography, especially its seascapes. [ABSTRACT FROM AUTHOR]