The molecular characterization of the parasitoid, Blaesoxipha rufipes was studied for the first time using cytochrome oxidase subunit I (COI) and the ribosomal 12S genes to assist with species identification. Parasitoid samples were collected from five localities to examine the molecular variability of B. rufipes in western Saudi Arabia. The partial 12S and COI sequences were investigated using two analytical methods (maximum-parsimony and neighbor-joining). The A, C, G and T base compositions were 37.9%, 10.6%, 14.5% and 37%, respectively, for the 12S genes, and 27.9%, 17.5%, 16.8% and 37.8%, respectively, for the COI genes. The pairwise genetic distances (D) among the studied populations ranged from 0.006 to 0.012 in the 12S gene and from 0.002 to 0.05 in COI gene. The sequence of COI showed 97 base substitutions among and within the populations. Of these substitutions, only one amino acid changed at position 189. The array of amino acid sequences resembles the sequences of previously studied species of Blaesoxipha. Consequently, it could be concluded that the studied populations of B. rufipes showed low genetic variability, indicating that fragmentation and/or other ecological factors have some impact on them.