Leishmaniasis and Carrion's disease are endemic neglected diseases in Peru. Both diseases are transmitted by phlebotomine sand flies competent for infection with Leishmania species and Bartonella bacilliformis. In Peru, 149 sand fly species have been identified. Knowledge regarding sand fly species diversity and distribution in leishmaniasis and Carrion's disease transmission areas has grown in the past 2 decades through multiple surveillance efforts in endemic regions, including unexplored low and high jungle areas. Furthermore, molecular testing approaches have been implemented to enhance surveillance of Leishmania and Bartonella species in sand fly populations from these endemic regions. This review emphasizes the importance of entomological surveillance in Peru for the characterization of sand fly species and the discovery of a great diversity of Leishmania and Bartonella species in sand fly populations from Andean and Amazonian regions.