The M and S forms of A. gambiae have been the subject of intense study, but are morphologically indistinguishable and can only be identified using molecular techniques. PCR-based assays to distinguish the two forms have been designed and applied widely. However, the application of these assays towards identifying hybrids between the two forms, and backcrossed hybrids in particular, has been problematic as the currently available diagnostic assays are based on single loci, and/or are located within a multi-copy gene. Here we present an alternative genotyping method for detecting hybridization and introgression between M and S molecular forms based on a multi-locus panel of single nucleotide polymorphisms (SNPs) fixed between the M and S forms. The panel of SNPs employed are located in so called “islands of divergence” leading us to describe this method as the “Divergence Island SNP” (DIS) assay. We show this multi-locus SNP genotyping approach can robustly and accurately detect F1 hybrids as well as backcrossed individuals.