Enteromius thysi (Trewavas, 1974) is an endemic and endangered African small barb distributed in Cameroon and Bioko, Lower Guinea. E. thysi previously belonged to the genus 'Barbus', with a long-standing dilemma in taxonomic classification. In this study, we provide the complete mitogenome of E. thysi from Cameroon using the typical primer walking and Sanger sequencing. The mitogenome of E. thysi (16,688 bp) consists of 37 genes, including 22 tRNA, 13 protein-coding genes, two ribosomal RNA genes and a AT-rich control region. The heavy strand accommodates 28 genes (12 PCGs, two rRNAs, and 14 tRNAs), however the light strand accommodates nine genes (NAD6 and eight tRNAs). The E. thysi mitogenome is AT biased (60.5%) as exhibited in other Enteromius species. Most of the PCGs start with ATG initiation codon except COI with GTG, whereas seven PCGs end with TAA termination codon except others with an incomplete termination codon. Most of the tRNAs showed classical cloverleaf secondary structures except tRNA-Ser1. The BA phylogeny distinctly separated E. thysi from other congeners and congruent with the earlier hypotheses. However, an uneven diversity and evolutionary pattern were remarked within the Enteromius species distributed in the North-western and South-eastern riverine systems, which need further investigation. More survey, in-depth taxonomy, and generation of other genetic markers (nuclear and mitochondrial) may resolve the diversification pattern of Enteromius species in Africa.