Samples of adult females of the Anopheles gambiae complex from thirteen localities of three islands of the Comoro Archipelago (Anjouan, Grande Comore and Moheli) were identified by analysis of ovarian polytene chromosomes as An. gambiae s.s. The samples showed only the inversion polymorphism 2La, the mean frequency of the inverted arrangement being 38%. A significantly higher frequency of the inverted arrangement 2La was observed in the localities with a lower annual rainfall. Similarities between the chromosomal polymorphism of the samples from Comoros and that of coastal eastern African countries suggest a probable continental origin of the An. gambiae s.s. populations in the Comoro Archipelago. A biometric analysis was carried out on the palpal index and the number of coeloconic sensilla, two characters partially diagnostic between fresh- and salt-water members of the gambiae complex. The palpal index of the 2La homozygous inverted females of An. gambiae s.s. was found to be significantly higher than the index of standard homozygotes and heterozygotes, suggesting a relation between the inversion and this biometric character. No An. merus was identified, although larvae of An. gambiae s.l. were observed breeding in brackish water.