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We have surveyed sympatric reptiles in a diverse and preserved montane environment in the Northern Dinaric region (Southern Slovenia) to determine the assemblage structure and assess the patterns of habitat segregation. Altitude and habitat type contributed the most to segregations between the most abundant species. The most similar were species pairs of L. viridis/bilineata and P. muralis, and I. horvathi and V. ammodytes. In snakes, significant segregation patterns have been observed between all species. Among lizards, we have found strong altitudinal segregation between two morphologically and ecologically most similar species; P. muralis was most abundant at low and I. horvathi at higher elevations. This result indicated a potential competitive interaction between these species.