The Persian leopard (Panthera pardus saxicolor) is an endangered species widely distributed across Iran. Rough estimates indicate 550–850 Persian leopard individuals inhabit the country, which comprises more than two thirds of its global population. Population monitoring of this large carnivore in Iran is one of the main objectives of current conservation planning. Therefore, adopting a more diversified methodology to achieve reliable, cost-effective, and pragmatic measures is urgently needed. We conducted a study for individual identification of the Persian leopard in Parvar Protected Area via fecal sampling and molecular tools and attempted to test the feasibility of this approach. We used 12 previously reported polymorphic microsatellite loci, of which only five were qualified for genotyping analysis. Finally, nine leopard individuals were identified. We measured the ability of the five loci in distinguishing individuals by P_(ID)sib. The cumulative observed probability of identity and probability of identity for sibling individuals were estimated to be 0.005 and 0.05, respectively. Data presented on spatial distribution of leopards in this study could help better understand the behavioral ecology and conservation biology of the species. Moreover, our findings will assist future research in developing methodologies for large-scale studies and providing data for effective wildlife conservation.