In Israel, sand flies are the vectors of Leishmania Ross and mosquitoes are the vectors of West Nile Virus. In the Judean Desert and Tiberias, the sand fly Phlebotomus sergenti Parrot is the vector of Leishmania tropica (Wright) and the rock hyrax (Procavia capensis Pallas) is considered the main reservoir animal. The main vectors of West Nile Virus are Culex pipiens L. and Culex perexiguus Theobald. Bloodmeals of engorged field-caught female sand flies and mosquitoes are an important source for defining host preferences. Recent progress in DNA molecular techniques has enabled the accurate identification of blood sources within the arthropod gut. In this study, we applied molecular approach for species-specific identification based on polymerase chain reaction and nucleotide sequence analysis of polymorphic regions along two mitochondrial genes, 12S and 16S rRNA. The research was carried out on 261 engorged female sand flies collected in the Judean Desert and Tiberias and 50 engorged female mosquitoes collected in Tel-Aviv and Arava. Species identification of bloodmeals was successful in 92% of the samples. Rock hyrax was the most abundant host in bloodmeals of P. sergenti, while human blood was found in only seven (3%) females. L. tropica DNA was detected in three P. sergenti females from Tiberias that contained rock hyrax blood. Avian sequences were detected in 67% (10 of 15) of the identified bloodmeals from Cx. perexiguus and in 10% (3 of 29) of the identified meals from Cx. pipiens. Human sequences were found in 14% of the identified bloodmeals from Cx. pipiens. The successful analysis of the majority of the bloodmeals performed on wild sand flies and mosquitoes suggests that bloodmeal identification can be applied as one of the routine procedures in vector surveillance programs.