Leishmania chagasi causes visceral leishmaniasis and, to a lesser extent, atypical cutaneous leishmaniasis in Central and South America. Its main sand fly vector, Lutzomyia longipalpis s.l. (Diptera: Psychodidae) displays a complex population structure that might contribute to the observed clinical pleomorphism and to recent major urban epidemics. This article summarises our understanding on reproductive barriers and hybridisation among this vector's sibling incipient species. Identifying genes important for sand fly ecological adaptability and sand fly-Leishmania genetic co-variation could be helpful for interrupting Leishmania transmission.