Background: Khorasan Province is an endemic region for cutaneous leishmaniasis. The species identification of Leishmania protozoa is useful for the control and prevention of leishmaniasis. Objectives: The present study is the first to identify Leishmania species by evaluating their risk factors in Quchan, Northern Khorasan, Northeast of Iran. Methods: A questionnaire and slide smears were collected from 103 individuals suspected of having leishmaniasis. Optimized PCR was performed using specific kDNA primers on all the slides. The data obtained were analyzed in SPSS-20 software. Results: Among the 103 subjects with skin ulcers suspected of having CL, 77 (74.8%) showed positive results in their direct microscopic smear. Specific Leishmania PCR bands, however, were observed in 86 (83.4%), including 57 subjects with L. tropica and 29 with L. major. The most frequent age range involved was 20-30 years and the most common site of the lesions was the hands. From the 57 cases of L. tropica, 43.9% and 56.1% lived in urban and rural districts, respectively. The sensitivity of microscopy for the diagnosis of Leishmania spp. was calculated as 89.5% in this study. Conclusions: L. tropica is the dominant causative species for cutaneous leishmaniasis in Quchan. This study identified a new rural focus for cutaneous leishmaniasis caused by L. tropica in Quchan suburbs.