Cutaneous Leishmaniasis (CL) is a major public health threat in Saudi Arabia with an average of 2500 cases per year (Abuzaid et al., 2017). The disease is caused by over 20 species of the genus Leishmania and manifests as ulcerating skin lesions that can lead to life-long scars (Abuzaid et al., 2017; Ministry of Health, 2019). Traditional parasitological techniques (e.g., microscopy and immunodiagnostics) are considered the gold standard; however, they cannot differentiate between the various Leishmania species. Although molecular techniques, such as polymerase chain reaction along with consecutive restriction fragment length polymorphism (PCR RFLP) or next-generation sequencing, can identify species of Leishmania (Domagalska et al., 2019), they have limited clinical use. A rapid and accurate Leishmania identification and classification protocol that can aid in clinical decision-making would be expected to meet a real clinical need. In this study, we identify Leishmania species directly from biopsy samples using Oxford nanopore sequencing technology (ONT).