We analysed the genetic diversity of nine populations of two subspecies of Sarotherodon melanotheron using allozymes in relation to the existence of environmental pressures. The genetic variability of Sarotherodon melanotheron melanotheron in the Ivorian ecosystem (A = 1.23, He = 0.04 and P-(95%) = 11.11) was lower than that of Sarotherodon melanotheron heudelotii of the estuaries in Gambia and Saloum (A = 1.68, He = 0.08 and P-(95%) = 22.23). The analysis of allelic diversity revealed that the individuals of S. m. melanotheron subspecies from a much polluted environment (lagoon of Grand-Lahou or Ebrie) presented a relatively higher frequency of allele GPI-2*80 than those of a less polluted environment (Aby lagoon and Ayame lake). The allele IDH-2*90 was expressed only in the specimens of S. m. heudelotii found in the Saloum estuary, a very saline environment compared to the estuary of Gambia. A deficit of heterozygosis was observed with the tilapia Sarotherodon melanotheron. This study confirmed the possibility of using allozymes as biomarkers and bioindicators of environmental disturbances.