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The complete mitochondrial genome of endangered <i>Enteromius thysi</i> was determined from Cameroon in Western Africa. The genome was 16,688 bp in length, comprising 37 genes (13 PCGs, 2 rRNAs, 22 tRNAs, and an AT-rich control region). The heavy strand accommodates 28 genes (12 PCGs, 2 rRNAs, and 14 tRNAs), whereas the light strand holds 9 genes (NAD6 and 8 tRNAs). The <i>E. thysi</i> mitogenome is AT-biased (60.5%), as exhibited in other <i>Enteromius</i> species. Most of the PCGs start with the ATG initiation codon, except <i>COI</i>, with GTG, and seven PCGs end with the TAA termination codon, except some with an incomplete termination codon. Most of the tRNAs showed classical cloverleaf secondary structures, except tRNA-serine (<i>trnS1</i>). Bayesian phylogeny distinctly separated <i>E. thysi</i> from other congeners. The control regions of <i>Enteromius</i> species exhibited highly variable nucleotides, and parsimony-informative sites were found in the conserved sequence block-III (CSB-III) compared with other domains and a unique 9 bp tandem repeat (ATGCATGGT) in the variable-number tandem repeats (VNTRs) region of <i>E. thysi</i>. The present phylogeny with limited mitogenomes showed an uneven diversity and evolutionary patterns of <i>Enteromius</i> species distributed in the northwestern and southeastern riverine systems in Africa, which warrants further investigation. Based on the results of the present study, we recommend additional surveys, in-depth taxonomy, and the generation of more mitogenomes that could resolve the diversification pattern of <i>Enteromius</i> species in Africa.