The commercial and economic importance of the mangrove oysters in the Lagos Lagoon provokes a great deal of biotic investigation, which provides a convincing justification for sequencing an oyster genome. Differentiating oysters based on their morphological characteristics for species identification and taxonomy is highly challenging because of the high intensity of phenotypic changes they exhibit. The genomic resources available for the mangrove oysters are incomparable to resources for any other bivalve invertebrates. In this study, unidentified mangrove oysters were collected from three different mangrove swamps off the Lagos Lagoon, Nigeria. Molecular procedures were used to identify the oysters genetically while pairwise and multiple alignments of mitochondrial DNA gene sequences of representative oyster strains within the clusters were used to relate them phenotypically to other oysters from various locations. Genetic diversity present in the selected mangrove oyster samples based on cytochrome oxidase I (COI) gene sequences reveals that the unidentified species at the three locations are Crassostrea gasar (Adanson, 1757) and were shown to be more like Brazilian oysters (Crassostrea brasiliana) with 99.55% similarity but clustered in a different clade of mangrove oysters in the GenBank. Similarities in the genetic makeup can principally be accredited to high levels of constant gene flow that are aftermaths of dispersal facilitated by a relatively long pelagic larval stage while the morphological differences can be primarily attributed to ontogeny with environmental conditions. A phylogenetic tree was constructed. The significance of these existing resources for a broad range of evolutionary and environmental sciences will be critically leveraged by having a recent or current genome sequence. The information obtained from this report is crucial to the understanding of diversity, systematics, and population genetics of mangrove oyster species of the Lagos Lagoon
