Species-specific differences encountered in the nucleotide sequences of a highly variable region of the 18S rRNA gene were used to design a multiplex polymerase chain reaction (PCR) assay for the identification of Phlebotomus papatasi Scopoli and Phlebotomus argentipes Annandale & Brunetti, vectors of Leishmania. This multiplex PCR assay uses a common forward primer and two reverse primers, which are specific for the two species. Amplification of a PCR product of size 788 bp indicates the presence of P. papatasi, whereas a product of size 677 bp indicates the presence of P. argentipes. The assay was found to be highly specific and sensitive.