Leishmaniasis is a neglected tropical parasitic disease affecting a large number of countries in the world. Early diagnosis of Leishmania infections is essential for therapeutic reasons, as it can decrease morbidity and mortality. L. siamensis and L. martiniquensis are novel Leishmania species recently described in Thailand and Myanmar. The disease is usually found in immunocompromised patients, especially those who have AIDS. Currently, the diagnosis of Leishmania infection in Thailand relies on microscopy, microbial culture, and polymerase chain reaction (PCR). In this study, we established a quantitative PCR (qPCR) method for detection of L. martiniquensis DNA in various types of clinical specimens, including whole blood, buffy coat, saliva, and urine of L. martiniquensis infected patients. The results of the qPCR assay were positive in all saliva samples. The assay is therefore effective to detect L. martiniquensis DNA even in noninvasive specimens, and it could be used for the diagnosis, follow up, and survey of L. martiniquensis infections.