Cutaneous leishmaniasis is considered as health problem in many parts of Iran such as Torbat-e Heydarieh in Khorasan Razavi province. Identification of the Leishmaniaspecies is useful for the control of this disease. Microscopic examination and clinical findings aren’t sufficient for the differentiation of the parasites. kDNA - PCR technique is a very reliable method to detect Leishmania species. The objective of this study the identification of leishmania species using PCR and compared to the routine microscopic examination in Torbat-e-Heydarieh. Slide smears obtained from skin lesions of 70 patients suspected to the leishmaniasis. Direct microscopy and an optimized PCR method were performed using specific kDNA primers. Data were analyzed with SPSS ver.16 software. Among 70 subjects with skin ulcers suspected to CL, 57(81%) were positive in direct microscopic smear examination. However, specific Leishmania PCR band were observed in 60(86%), in which 53 subjects had L. tropica and 7 has L. major. Although, gender and age distribution does not show any statistically significant differences, the seasonal occurrence of the infection in autumn was significant (P <0.05). The most common site of lesions was the face (37%) (P <0.05). Sensitivity of kPCR for diagnosis Lashmaniaspp was calculated 95% in this study. Optimized PCR method revealed that both genus of Lashmania are prevalent in the of Torbat-e Heydarieh in which L. tropica is the dominant causative species for cutaneous Leishmaniasis.