The aim of this study was to establish the genetic studies of the population from one of the most important known aboriginal funerary spaces of the island of El Hierro (Canary Islands), the Punta Azul cave, which harbors remains of 127 individuals. Sixty-one adult tibiae were examined, 32 left and 29 right. Radiocarbon dating yields an antiquity of 1015-1210 AD. We have obtained an overall success rate of 88.5% for the molecular sexing, and of 90.16% for the uniparental markers. Short tandem repeats (STR) profiles were also possible for 45.9% of the samples. This performance is a consequence of the good conservation of the bones in their archaeological context. The mtDNA composition of the sample is characterized by the complete fixation of the H1-16260 lineage. These results can be explained by a mixture of consecutive founding events, a bottleneck episode at the beginning of the colonization and/or as a consequence of genetic drift. Paternal lineages were also affected by these processes but in a less acute way. These differences lead us to propose social behaviors as an explanation for this difference. The maternal transmission of the lineages, mentioned in ethnohistorical sources of the Archipelago, could be an explanation. These results could be in agreement with endogamous practices, but the autosomal STR results indicate a relative high diversity. These results have allowed us to characterize the Punta Azul cave population and see the way in which geographical isolation, the process of adaptation and specific social behaviors affected the aboriginal population of the Island. (C) 2016 Elsevier Ltd. All rights reserved.