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Forty-four (44) samples of clams were obtained from three locations between Cross River and Akwa Ibom States. Genomic DNA was extracted from tissues of the clams using cetyl trimethylammonium bromide (CTAB). Following DNA extraction from the tissues, ultraviolet radiation spectroscopy was used to get the concentration of the DNA isolated from the tissue. From the study, the mean gene diversity obtained was 0.8950 while polymorphic information content was 0.8860. A dendogram of the 44 samples using Weighted Neighbour – Joining (WNJ) procedure clustered them into four major groups. Group I had 78% bootstrap value, group II had 85% bootstrap value, group III had 74% bootstrap value, while group IV had 80% bootstrap. The results of genetic study of the three populations of Egeria radiata showed that they were diverse. Similarly, the principal component analysis (PCA) indicated that the four(4) clusters had samples across all the populations of clams studied, showing that there was an active migration of the clams among the three populations leading to a high genetic diversity of the clams. The implication of the results taking together showed that further genotyping should be carried out using other DNA markers that could add further understanding to the genetic diversity of clams.