The Strait of Gibraltar is inhabited by around 216 pilot whales, which are present all year round, and nothing is known about their social structure. The aim of this study is to analyse the inter-individual association patterns within this pilot whales community to (1) provide an insight on their long-term social system and (2) to assess the relationship between sexes within this social system. Between 1999 and 2006, 23,004 km was sampled in the Strait of Gibraltar, and 4,887 images of dorsal fins of pilot whales were taken from 226 groups. The sex of 56 of the individuals could be determined genetically. The strength of the behavioural relationships between dyads of individuals was calculated, and the temporal aspects of the social structure were evaluated, showing in a non-random social structure made by constant companions. The preferred associations between individuals consisted in associations of males-females. Eight long-term units could be found with different degrees of association rates. Consequently, we propose that, in the Strait, the pilot whales exhibit a hierarchical social system composed of a population encompassing several clans of pilot whales each containing several pods. Pods will then be formed by several line units, similar to killer whale matrilineal units.