A method of typing Phlebotomus taxa in three areas in Saudi Arabia (Riyadh, Madinah and Asir) using morphological characteristics revealed that the phlebotomine species is Phlebotomus papatasi. This identification was confirmed by establishing a polymerase chain reaction (PCR) and  direct  partial sequences of 18S ribosomal RNA (rRNA) gene using specific designed Primers SandF1:5′-AGGCTCATTCAGTCGCTTTC-3′ and SandR1:5′-TGCAAGCTTATGACTCACACTT-3′. Morphological individual variations were also observed among some collected specimens. Nevertheless, genetic analysis confirmed that these specimens were also P. papatasi. PCR-amplified amplicons   using ChromasPro. MEGA 5 program and neighbor joining (NJ) methods revealed several direct sequences for P. papatasi that were submitted in GenBank under the accession number JQ929125. In conclusion, the obtained results establish a powerful tool for the molecular taxonomy of Phlebotomus spp. in endemic areas to plan appropriate epidemiological surveillance programs that could be used to detect natural infections of sand fly vectors with pathogens.