Identification of new foci of cutaneous leishmaniasis (CL), along with reports of Leishmania donovani causing the disease, is an issue of concern. Clinico-epidemiologic analysis of 98 cases in the endemic regions of Rajasthan state, India, suggested the preponderance of infection in men (62.24%) compared with women (37.75%). Species characterization by internal transcribed spacer 1 (ITS1) polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP), kDNA-PCR, and immunofluorescence assay established L. tropica as the causative organism. When applied directly to 32 clinical samples, kDNA PCR had a sensitivity of 96.6%, whereas ITS1 PCR had a sensitivity of 82.75%, thus facilitating diagnosis and species identification. Either parasite culture or direct microscopy alone detected 48.2% and 65.5% of the positive samples, respectively, whereas culture and microscopy together improved overall sensitivity to 89.3% (25/28). Except for the kDNA PCR, all other assays were 100% specific. This study provides the first comprehensive molecular and immunologic studies of CL in India.