Space use including territoriality and spatial arrangement within a population can reveal important information on the nature, dynamics and evolutionary maintenance of alternative strategies in colour polymorphic species. Despite the prevalence of colour polymorphic species as model systems in evolutionary biology, the interaction between space-use and genetic structuring of morphs within populations has rarely been examined. Here we assess the spatial and genetic structure of male throat colour morphs within a population of the tawny dragon lizard, Ctenophorus decresii. Male colour morphs do not differ in morphology but differ in aggressive and anti-predator behaviours as well as androgen levels. Despite these behavioural and endocrine differences, we find that colour morphs do not differ in territory size, with their spatial arrangement being essentially random with respect to each other. There were no differences in genetic diversity or relatedness between morphs; however, there was significant, albeit weak, genetic differentiation between morphs, which was unrelated to geographic distance between individuals. Our results indicate potential weak barriers to gene flow between some morphs, potentially due to non-random pre- or post-copulatory mate choice or postzygotic genetic incompatibilities. However, space use, spatial structure and non-random mating do not appear to be primary mechanisms maintaining colour polymorphism in this system, highlighting the complexity and variation in alternative strategies associated with colour polymorphism.