Marxan, a complementarity based area selection software, was used to detect the priority protected areas for the Lesser Caucasus Ecoregion. Six taxonomic groups, endemic and non-endemic highly threatened plants, globally important amphibian and reptiles, butterflies, breeding birds, large mammals, and ecological communities were included in the analysis. Nineteen areas (planning units) were identified as priority protected areas among 336 planning units (UTM grids) of 10 x 10 km. The efficacy of the identified priority areas were measured with species representation. Also, distributions of the priority areas were compared with existing protected area systems of the study area. Results indicated that priority protected areas achieved higher than 70% species representation for taxonomic groups and distributions of priority areas were very consistent with existing protected area systems. The Marxan program produced compact complementary priority protected areas. These priority protected areas provided the maximum species representation for the study area. Moreover, results showed the importance of already existing protected areas and determined the need for new protected areas.