The study evaluated the use of PCR method to detect Leishmania parasite in microscopy-negative samples from patients suspected of cutaneous leishmaniasis. A total of 131 samples from patients in Iran collected between March 2013 and February 2015 were analyzed. PCR detected Leishmania DNA in 34 samples (25.9%), with 23 samples (67.6%) identified as L. major and 11 samples (32.4%) as L. tropica. All L. major-positive samples originated from Gonbad-e-Qabus, while all L. tropica-positive samples came from Torbat-e-Jam. Most PCR-positive lesions (79.4%) were chronic, secondarily infected, or clinically atypical. The results suggest that PCR analysis can serve as a useful second-line test for confirming diagnosis and determining parasite species, particularly in chronic or atypical lesions.