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The African catfish <i>Clarias gariepinus</i> has been introduced for aquaculture in Bangladesh due to the scarcity of indigenous <i>C. batrachus</i> fingerlings. However, the government of Bangladesh has banned the farming of <i>C. gariepinus</i> due to the carnivorous nature of this species. Recently <i>C. gariepinus</i> has been reported by fish farmers and consumers in Bangladesh, and unplanned hybridization between native and exotic species has been suspected. This study attempts to know the purity of <i>C. batrachus</i> by analyzing mitochondrial genes. Both directly sequenced and retrieved Cytochrome C Oxidase subunit I (COI) and cytochrome b (Cytb) genes from <i>C. gareipinus</i> and <i>C. batrachus</i> were analyzed by MEGA software. The morphologically dissimilar <i>C. batrachus</i> showed the least genetic distance (0.295) from <i>C. gariepinus</i>, which provided evidence of hybridization between the two species. Maximum likelihood (ML) phylogenetic trees showed that <i>C. batrachus</i> from Bangladesh did not cluster with <i>C. batrachus</i> of other countries, instead <i>C. batrachus</i> clustered with the exotic <i>C. gariepinus</i>. The suspected hybrid formed sister taxa with the exotic <i>C. gariepinus</i>. The study corroborates the genetic deterioration of <i>C. batrachus</i> by unplanned hybridization with the invasive <i>C. gariepinus</i>. Unplanned hybridization has deleterious consequences; therefore, immediate action is necessary for aquaculture sustainability and biodiversity conservation in Bangladesh.