Three species of the Anopheles gambiae complex were identified in Guinea Bissau (West Africa) by chromosomal analysis. They were An. melas, An. arabiensis and An. gambiae s.s. An melas was observed in coastal and insular zones of the study area as well as in areas where the rivers are tidal and brackish and bordered by mangroves. For this reason, the species occurs also in inland riverine localities such as Farim and Bissorà. An. arabiensis apparently occurs only in low numbers in a very limited inland area during the dry season. An gambiae s.s. was observed nearly everywhere in the study area. In the samples of An. melas three inversion polymorphisms occurred: one on the chromosomal arm 2R (2Rn) and two on the arm 3R (3Rc and 3Re). It was observed that the frequencies of the inverted arrangements 2Rn and 3Re were significantly higher in the islands as compared to the continental sampling localities. The An. arabiensis sample was characterized by the presence of three inversion polymorphisms: 2Ra, 2Rb and 3Ra. A very high degree of polymorphism was shown by the An. gambiae s.s. samples. Four inversion polymorphisms were observed (three on chromosomal arm 2R and one on arm 2L) with very different frequencies of the alternative arrangements in different zones of the study area. From these data it seemed possible to split the species into three populations, each of them apparently linked with a peculiar ecological situation. The first population, characterized by high frequencies of 2Rd arrangement, is present on the coastal zones and in the islands; the second one is present in the northern inland areas particularly during the dry season and it is characterized by high frequencies of 2Rb and 2La arrangements. The third population is present only in the inland zones and it is characterized by high frequencies of 2Rjb, 2Rjd and 2Rjbd arrangements.