Kin relations among past societies can offer valuable information about the social dynamics of the population. Genetic data from prehistoric human remains can reveal genetic relatedness, and when combined with archaeological information, shed light on social factors shaping ancient communities. However, accessing such information on ancient hunter–gatherer societies has been challenging owing to the scarcity of temporally overlapping multi-burial sites. Here, we focused on the Pitted Ware Culture (PWC) cemetery from Ajvide (Gotland, Sweden), one of Stone Age Europe’s largest and best-preserved hunter–gatherer burial grounds of the European Stone Age. We generated new genomic data from 10 individuals, primarily from co-burial contexts, and combined these with published genomes from 24 individuals across four PWC sites on Gotland. The genetic analyses revealed dual ancestry of the Gotlandic PWC, showing approximately 80% ancestry associated with earlier Mesolithic hunter–gatherer groups and 20% with farmer groups. We also identified close genetic relatives between the different studied PWC sites on Gotland, indicating mixing of the groups. All individuals buried together were closely related to one another, including first-, second- and third-degree relatives, and showed significantly elevated genetic relatedness. This demonstrates that genetic relatedness played a defining role in the co-burial ritual and extended beyond first-degree relatives.