With the increasing human population world-wide, animals and humans are sharing more habitat. In this study, we consider the consequences of this habitat usage overlap on the behaviour patterns and social structure of a threatened species. Specifically, we used focal animal samples to collect data on the Cuban rock iguana, Cyclura nubila, in six field sites. Three of these sites are subject to considerable anthropogenic habitat usage, whereas three are in relatively low anthropogenic usage areas. Individuals in high anthropogenic usage sites were more closely assembled, with more males and females sharing a smaller amount of space. These animals exhibited even more aggressive behaviour and social interactions than expected when taking into account the larger number of possible interactants. High anthropogenic usage sites also had more male–male interactions and fewer males interacting with females. We suggest that social and mating system changes have occurred. Ramifications of these recent changes in the behavioural repertoires on the long-term survival of the species are discussed.