Leishmaniasis is an emerging disease in Thailand. Herein, we report on two human immunodeficiency virus (HIV)-infected patients with leishmaniasis who presented with overlapping manifestations between cutaneous and visceral leishmaniasis. Sequencing analysis of the internal transcribed spacer 1 (ITS1) of the ribosomal RNA gene showed that the species was identical to a new species recently described in Thailand. The detection of DNA of this Leishmania species in saliva may have important implications for transmission and epidemiological studies.