© 2020, Witold Stefański Institute of Parasitology, Polish Academy of Sciences.Sanliurfa, a city in southeastern Turkey, is host to 477,166 Syrian refugees. The incidence of cutaneous leishmaniasis (CL) may be on the rise in areas affected by a refugee crisis, like Sanliurfa; thus, consequently, local uncommon species of Leishmania may be encountered in these regions. This might potentially make diagnosis and treatment more challenging over time. In this study, it was aimed to identify the causative agents of CL in clinical samples. A total of 154 patients (60 Syrian and 94 Turkish) who were diagnosed with CL via microscopical examination and PCR were enrolled this study. All of the samples were analyzed using internal transcribed spacer 1 genes, restriction fragment length polymorphism, DNA-sequencing, and phylogenetic analyses. In this study, Leishmania tropica was determined to be the predominant species in 140 of the patients (90.9%), followed by Leishmania major in 12 patients (7.8%), and Leishmania infantum in 2 patients (1.3%). Of the 94 Turkish patients, 94.7% were infected with L. tropica and 5.3% were infected with L. major, while none were infected with L. infantum. However, of the 60 Syrian patients, 85% were infected with L. tropica, 11.7% were infected with L. major, and 3.3% were infected with L. infantum. There was a significant association between the Leishmania species and the nations (Turkish–Syrian) (P < 0.001). The sequences were numbered from MH347941 to MH347953 and submitted to GenBank. This study confirmed that L. tropica, L. major, and L. infantum coexisted in Sanliurfa. This was the first time that the species L. infantum was reported among recent immigrants from Syria in Sanliurfa. Therefore, it is necessary to discriminate the Leishmania species for diagnosis, treatment, and controlled studies in hyper-endemic regions.