The Neotropical region currently harbors 8 recognized species of small cats, including the margay (Leopardus wiedii) and jaguarundi (Puma yagouaroundi). These similar-sized species have broad geographic distributions and commonly occur in sympatry. We constructed species occurrence databases and used the maximum entropy (Maxent) modeling approach to develop models of habitat suitability for each of these species. We identified the environmental predictors with the highest importance for species occurrence and evaluated how they influence habitat suitability for both wild cats. Variables related to temperature and precipitation were good predictors of species occurrence, with both cats responding similarly to them. However, margay showed higher variation in habitat suitability depending on local climatic predictors. The estimated models indicated high niche similarity (> 76%) between these cats, but despite this we identified different areas with the most favorable conditions for each species’ occurrence. Approximately 50% and 72% of the entire suitable area were estimated as being moderately to highly suitable for margay and jaguarundi, respectively, with the margay model comprising a higher proportion of forest environments in comparison to that of the jaguarundi. These findings will be relevant in the context of conservation planning when indicating the priority areas for their long-term preservation.