The mosquitoes of the Anopheles gambiae complex have been characterised at specific and sub-specific levels in two islands of the Comoros archipelago: the island of Mayotte (French departmental collectivity) and the island of Grande Comore (Comoros Union). Results are similar in the two islands and are presented together. The species An. gambiae s.s. was observed alone (determination performed on 149 specimens by PCR product of IGS of rDNA). The molecular form observed alone was S, and corresponds in this geographic area to the chromosomal form Savanna (determination performed on 123 specimens by another PCR product of IGS of rDNA). The haplotype IB was observed alone (determination performed on ten specimens, by sequencing the ITS of rDNA, with special attention at the position 871 of ITS), as previously observed by other authors in East Africa. Finally, in Mayotte and Grande Comore the An. gambiae complex is only composed by An. gambiae s.s. from the molecular form S/type IB.