The study on the phenotypic polymorphism of Heterotis niloticus was undertaken from February to May 2020 in the rain forest region of Cameroon. The  main objective was to contribute to a better understanding of the genetic diversity of this adapted species for adequate breeding and preservation  strategies. More specifically, the investigation aimed at evaluating the variability of phenotypic, morphometric and meristic features according to the  study sites. Further, it was also in order to analyse the phenotypic variability, the structure, as well as the phylogenetic relationships among the Heterotis  niloticus subpopulations. A total of 125 adult individuals were collected in three localities and characterized. Two (2) phaneroptic traits were observed,  while 16 morphometric traits were measured and 5 meristic characters were counted. The results showed that there is a colour variability of eyes and  body in Heterotis niloticus from the study area with a predominance of golden eyes (97.60%) and grey body (96.80%). The number of scales on the lateral  line was higher in the individuals collected in Mbalmayo (38.67±1.46) than those in Ayos (37.70±0.95). Discriminant factor analyses and phylogenetic  analyses revealed that the overall population studied is made up of 3 morphotypes cohabiting in the three localities; thus it was possible to establish the  phylogenetic relationships that exist between them. Morphotypes 1 and 2 are closer while morphotypes 2 and 3 are far apart, showing a tendency of  splitting genetic make up. The recorded diversity suggests that Heterotis niloticus from the study area constitutes a natural genetic resource having the  interesting variability for further improvement and sustainable management.