Intraspecific variation as a way to explore factors affecting the evolution of species traits in natural environments is well documented, and also important in the context of preserving biodiversity. In this study, we investigated the extent of behavioural, morphological and ecological variation in the peninsula dragon (Ctenophorus fionni), an endemic Australian agamid that displays extensive variation in colour across three allopatric populations. The aims of the study were to quantify variation across the different populations in terms of the environment, morphometric characteristics and behaviour. We found population level differences in habitat structure and encounter rates. Adult body size of C. fionni, as well as a range of morphometric traits, differed between populations, as well as the frequency of social interactions, which appears to be related to population density and abundance. Analysis of communicative signals showed differences between the southern and central populations, which appear consistent with variations in response to environmental differences between study sites. The findings of the present study, coupled with previous work examining colour variation in this species, show that the three populations of C. fionni have likely undergone substantial differentiation, and would make an interesting study system to explore trait variation in more detail.