AbstractThe jaguarundiPuma yagouaroundiis a small Neotropical cat that presents two main coloration phenotypes (grey/dark vs. reddish). Although these coat colour variants have been known for decades, and historically speculated to be associated with different habitats, their exact geographical distribution has never been mapped. Moreover, their association to different habitats has so far not been tested statistically, so that their ecological relevance with respect to varying environmental features remains unknown. Based on 566 location records encompassing the entire historical range of the species obtained from camera‐traps, captures and skins held in scientific collections, we produced suitability models for both jaguarundi phenotypes using maximum entropy algorithms of niche modelling. The frequency of grey/dark jaguarundis isc. 80%, whereas reddish animals representc. 20% of our overall sample set. However, there were marked differences in these frequencies across regions. Although the spatial distribution of grey/dark animals did not depart substantially from random expectations (as it encompassed the whole species range), the occurrence of the ancestral reddish form was strongly and significantly non‐random. In spite of their broad distribution across multiple habitats, grey/dark animals were significantly associated with moist and dense forests, whereas reddish forms were associated with dry and open areas such as deserts and xeric landscapes. Furthermore, there were clear spatial differences in the suitability models generated for these coat colour phenotypes. We also employed the distribution models to investigate whether particular environmental predictors could explain these different distributions. Predictors related to moisture were especially influential on the differences between the grey/dark and reddish models, and demonstrate an effect of natural selection on coloration traits, suggesting that a complex interplay of different ecological processes regulates this system over evolutionary time.