Despite appreciable advances in carnivore ecology, studies on small cats remain limited with carnivore research in India being skewed towards large cats. Small cats are more specialized than their larger cousins in terms of resource selection. Studies on small cat population and habitat preference are critical to evaluate their status to ensure better management and conservation. We estimated abundance of two widespread small cats, the jungle cat, and the rusty-spotted cat, and investigated their habitat associations based on camera trap captures from a central Indian tiger reserve. We predicted fine-scale habitat segregation between these sympatric species as a driver of coexistence. We used an extension of the spatial count model in a Bayesian framework approach to estimate the population density of jungle cat and rusty-spotted cat and used generalized linear models to explore their habitat associations. Densities of rusty-spotted cat and jungle cat were estimated as 6.67 (95% CI 4.07-10.74) and 4.01 (95% CI 2.65-6.12) individuals/100 km2 respectively. Forest cover and evapotranspiration were positively associated with rusty-spotted cat occurrence whereas both factors had a significant negative relation with jungle cat occurrence. The results directed habitat segregation between these small cats with affinities of rusty-spotted cat and jungle cat towards well-forested and open scrubland areas respectively. Our estimates highlight the widespread applicability of this model for density estimation of species with no individual identification. Moreover, the study outcomes can aid in targeted management decisions and serve as the baseline for species conservation as these models allow robust population estimation of elusive species along with predicting their habitat preferences.