Background and aim: Isfahan is one of the most important endemic areas of zoonotic cutaneous leishmaniasis (ZCL) in Iran. The objective of this study was to present different clinical pictures of ZCL and to identify the responsible Leishmania species using polymerase chain reaction (PCR). Materials and methods: This cross-sectional, descriptive-analytic study was performed from September 2006 to February 2007, in skin Disease and Leishmania Research Center, which is a referal center for leishmaniasis. Among 440 suspected patients, Leishmania promastigotes were isolated from 31 atypical and 60 classic CL lesions and identified using Permissively Primed Polymorphic-PCR method. Results: From a total of 600 observed patients, 440 were parasitologically proved using direct smear, 409 patients (92.9%) showed typical clinical picture of volcano-shape and 31 (7.1%) of patients showed atypical forms. PCR method identified all isolates as L.major. Conclusion: ZCL lesions may present with various clinical manifestations in the same endemic area, which limits the identification of responsible parasite based on clinical features. The reason for diversities in clinical pictures are not yet known.