A polymerase chain reaction (PCR)-based diagnostic assay was developed that rapidly and reliably differentiates the sibling species of the Anopheles claviger complex, An. claviger s.s. and An. petragnani. The assay makes use of nucleotide differences in the internal transcribed spacer 2 ribosomal DNA sequences to generate PCR products of specific length for each of the two species. In evaluating the test, 580 of 592 field-collected An. claviger s.l. specimens were unambiguously identified as one of the two sibling species. Due to poor DNA quality, the remaining 12 specimens yielded no PCR product. Of the 592 mosquitoes, 407 larval specimens had been identified morphologically prior to species-specific DNA amplification, and in all instances PCR identification corroborated with morphologic identification. Mosquitoes identified as An. claviger s.s. came from various localities all over Europe and from Israel. Those identified as An. petragnani were collected in southern France and Spain. The species-diagnostic PCR assay would facilitate data collection on the temporal and spatial distribution of the two An. claviger sibling species because they represent possible vectors of disease in Europe, the Near and Middle East, and north Africa.