The mitochondrial genome (or mitogenome) is generally known for its compact size and conserved gene content in vertebrates (13 protein-coding, 22 tRNA, two rRNA genes, and the control region). Still, recent studies suggest that mitogenomes are more diverse, with repeats and duplication being more frequent than initially reported. This is observed in birds and reptiles, and to a lesser extent also in fish (e.g. gene duplication in icefishes). We are currently investigating the evolutionary relationships between eastern African species of Enteromius (Cyprinidae; 216 species) in the Lake Edward basin. We acquired a whole genome sequencing dataset, covering the known diversity of the genus in the system. We sequenced 22 specimens of nine highly divergent mitochondrial lineages within what are currently considered as five species (Illumina, 2x150 bp, 15 20x). We assembled the different mitogenomes and quality-checked them for signatures of duplication using NOVOPlasty. Within the nine lineages, we detected signatures of at least two independent events of duplication of the control region and ribosomal gene(s). Because of the high prevalence of these cases within the limited number of Enteromius species investigated, our results support that the occurrence of such phenomena might be widespread in this species-rich genus. This requires specific attention in future research, which should include long reads to clarify mitogenome structure. Linking our observations with the biology of the species remains highly speculative but they might suggest relaxed purifying selection.