Understanding the factors that affect hybridization is an important issue in the study of species evolution. In this work, we analyse the genetic structure of two lizard species, Salvator merianae and Salvator rufescens, at a microscale within a climatic niche analysis framework, to reveal the main factors that contribute to the stability of their hybrid zone. We assess the effect of climate in hybridization by quantifying and decomposing the niche overlap of both species. Using a mitochondrial and a nuclear marker, we find that hybridization is frequent and is not restricted to the sympatric region. The gene flow is mainly from S. rufescens to S. merianae, with introgression into the range of S. merianae. Also, S. merianae would have long been present in the area, while S. rufescens appears to be a recent colonizer. The climate contributes to the population structure of S. merianae, but not to that of S. rufescens. The niches occupied by S. rufescens in the hybrid zone and the non-hybrid zone are similar, while the niches of S. merianae are different. Our results do not fit previous models of hybrid zone stability, suggesting the need to develop new models that consider the evolutionary factors that can differentially affect parental species and hybrids.