This paper examines the role of kinship and postmarital residence in the emergence of organised cemeteries during the transition from the Final Neolithic to the Early Bronze Age at Marathon, Attica. Focusing on the cemetery of Tsepi, we performed intra‐cemetery biodistance analysis to test whether biological relatedness structured spatial organisation of tombs, and whether postmarital residence was matrilocal or patrilocal. Dental metric, dental morphological and cranial non‐metric data were collected from 293 individuals and subjected to multivariate analysis (principal component analysis, Euclidean distance ordination via multidimensional scaling), binomial probability calculations, Ripley's K analysis and determinant ratio analysis. Results indicated phenotypic similarity among some tomb co‐interments; however, outliers suggested that within‐tomb burial depended on a variety of factors that could include affinal, fictive or practical kinship. There was strong evidence for phenotypic patterning by tomb row, indicating that cemetery structure at Tsepi was organised according to biological lineages. This was especially evident for females. Male phenotypic variation was higher than that of females, though not significantly so. The results of intra‐cemetery biodistance analysis at Tsepi reveal a complex mortuary programme that emphasised biological kinship within an exogamous and likely matrilocal system of mate exchange. When considered in light of ethnographic evidence, the practice of male exogamy may correlate with the coastal location of the community and the maritime activities that structured the economy during the emergence of social complexity in the region. This paper illustrates the potential of biodistance analyses for elucidating aspects of social life in the Aegean. Copyright © 2017 John Wiley & Sons, Ltd.