Mislabelling of fish and fish products has attracted much attention over the last decades, following public awareness of the practice of substituting high-value with low-value fish in markets, restaurants, and processed seafood. In some cases, mislabelling includes illegal, unreported, and unregulated (IUU) fishing, contributing to overexploit substitute species that are undetectable when sold under wrong names. This is the first study of DNA barcoding to assess the level of mislabelling in fish marketed in Ghana, focusing on endangered shark species. Genetic identification was obtained from 650 base pair sequences within the cytochrome c oxidase I (COI) gene. All except one of 17 shark fillets analysed were wrongly labelled as compared with none of 28 samples of small commercial pelagic fish and 14 commercial shark samples purchased in Europe. Several substitute shark species in Ghana are endangered (Carcharhinus signatus and Isurus oxyrinchus) and critically endangered (Squatina aculeata). Shark products commercialized in Europe (n = 14) did not reveal mislabelling, thus specific shark mislabelling cannot be generalized. Although based on a limited number of samples and fish markets, the results that reveal trade of endangered sharks in Ghana markets encourage Ghanaian authorities to improve controls to enforce conservation measures.