The United Arab Emirates (UAE) has been identified as an active international seafood market. To identify some of the key fish species in the UAE markets, 9 species of fresh fishes were randomly collected from Souq Al Jubail in Sharjah City, one of the biggest fish markets in UAE. The samples were subjected to DNA barcoding using partial sequencing of the hypervariable 5´ region of the cytochrome oxidase subunit I (coi) gene. Furthermore, the results were phylogenetically analyzed to provide further accurate species identification. Genetic and phylogenetic analyses resolved the naming discrepancies found in 30% of the fishes. Genetic diversity within each species exhibited a general trend for high haplotypes´ diversities. Most haplotypes were shared with the Sea of Oman and the Arabian Gulf, and few with the Red Sea. The results strongly recommend continuous application of molecular-based species inspection in the UAE seafood markets for assuring authenticity, traceability, and proper conservation of the native species.