The nature and distribution of political power in Neolithic Europe remains poorly understood. During the period, many societies began to invest heavily in monument-building, suggesting an increase in social organisation. The scale and sophistication of megalithic architecture along the Atlantic seaboard is particularly impressive, culminating in the great passage tomb complexes. While megalith builders have often been proposed as co-operative networks of independent communities, the human expenditure required for the largest monuments has led some to emphasize hierarchy, the most extreme case being a small elite marshalling the labour of masses. Here we present evidence that such a social stratum was established over the course of the Irish Neolithic period. In a sampling of 44 whole genomes, we identify the adult son of a first-degree incestuous union discovered within the most elaborate recess of the imposing Newgrange passage tomb. Socially sanctioned matings of this nature are highly rare and occur almost exclusively among politico-religious elites, specifically within polygynous and patrilineal royal families headed by god-like kings. We identify relatives of this individual within two other major passage tomb complexes 150km to the west, as well as dietary differences and unprecedented fine-scale haplotypic structure between passage tomb samples and the larger population, implying a powerful and enduring hierarchy. We show this system emerged against a backdrop of rapid maritime colonisation, which displaced a unique Mesolithic isolate population, although a single Neolithic individual whose ancestry is partially derived from Irish hunter-gatherers is detected.