Sand flies are key vectors of parasitic protozoans of the genus Leishmania, some of which are causative agents of human leishmaniases. To fully understand a transmission cycle in a focus of leishmaniasis and possibly disrupt this cycle, it is of paramount importance to conclusively identify sand fly species present in the focus and assess their role in transmission. Species identification and taxonomy of sand flies is complicated by the fact that analysis of distinctive morphological characters requires expertise in assessment of minute and often obscured characters. This situation opens door for deployment of molecular methods to complement traditional morphology in integrative taxonomical approach. We use DNA sequencing of nuclear and mitochondrial markers including DNA barcoding as well as MALDI-TOF protein profiling which we pioneered for sand fly taxonomy.