Amplification of internal transcript spacer 1 of ribosomal RNA (ITS1-RNA) gene followed by RFLP analysis and sequencing was used to identify the causing agents of cutaneous and visceral leishmaniasis (CL and VL) in humans and animal reservoir hosts from various geographical areas in Iran. We also used random amplified polymorphic DNA (RAPD-PCR) to obtain polymorphisms among isolates ofLeishmaniaspp. Totally, 362 suspected human and animal cases including 173 CL, 49 VL, 60 rodents, and 80 domestic dogs were examined forLeishmaniainfection. From 112 culture-positive samples prepared from CL cases, 75 (67%) were infected withL. majorand 37 (33%) withL. tropica. Of the 60 rodents examined, 25 (41.6%) harbored theLeishmaniainfection; 21 were infected withL. majorand 4 withL. turanica. From 49 suspected VL, 29 were positive by direct agglutination test (DAT), whereas microscopy detected parasite in bone marrow of 25 and culture in 28 of the patients. Two VL patients were infected withL. tropicaand 26 withL. infantum. Of the 80 domestic dogs, 56 showed anti-Leishmaniaantibodies with DAT. Of these, 55 were positive by both microscopy and culture. Molecular identity, obtained only for 47 samples, revealedL. infantumin 43 andL. tropicain 4 dogs. The polymorphisms amongL. tropicaandL. majorisolates were 3.6% and 7.3%; the rate among human and canine VL isolates was 2.8% and 9.8%, respectively. Our results showed that at least four differentLeishmaniaspecies with various polymorphisms circulate among humans and animal hosts in Iran.