Four microsatellite markers were used to study genetic variation among individuals of the mouthbrooding tilapia Sarotherodon melanotheron (Rüppel 1852) caught in separate but adjacent shoals. A comparison was also made with fish from six other localities. Populations originating from riverine environments appear to be panmictic, while samples from open waters such as lagoons showed highly significant heterozygote deficiencies. For instance, at the 33-allele locus SMEL4, 32 homozygous individuals were observed among the 82 individuals from the same lagoon location instead of only five homozygotes expected if random mating occurred. A further assessment of the genetic similarity of individuals within each shoal, validated by robust permutation techniques requiring no precise knowledge of gene frequencies, showed that related individuals tend to aggregate, and suggested that mating occurs preferentially within small groups of kin. Cichlids are often presented as a group of fish where microallopatric speciation takes place. The possible link between kin aggregation, inbreeding and shoaling behaviour we propose here may have important consequences for our understanding of the mechanisms involved in this fast speciation process.