This study examines the utility of morphology and DNA barcoding in species identi-fication of freshwater fishes from north- central Nigeria. We compared moleculardata (mitochondrial cytochrome c oxidase subunit I (COI) sequences) of 136 de novosamples from 53 morphologically identified species alongside others in GenBank andBOLD databases. Using DNA sequence similarity- based (≥97% cutoff) identificationtechnique, 50 (94.30%) and 24 (45.30%) species were identified to species level usingGenBank and BOLD databases, respectively. Furthermore, we identified cases oftaxonomic problems in 26 (49.00%) morphologically identified species. There werealso four (7.10%) cases of mismatch in DNA barcoding in which our query sequencein GenBank and BOLD showed a sequence match with different species names.Using DNA barcode reference data, we also identified four unknown fish samplescollected from fishermen to species level. Our Neighbor- joining (NJ) tree analysisrecovers several intraspecific species clusters with strong bootstrap support (≥95%).Analysis uncovers two well- supported lineages within Schilbe intermedius. TheBayesian phylogenetic analyses of Nigerian S. intermedius with others from GenBankrecover four lineages. Evidence of genetic structuring is consistent with geographicregions of sub- Saharan Africa. Thus, cryptic lineage diversity may illustrate species’adaptive responses to local environmental conditions. Finally, our study underscoresthe importance of incorporating morphology and DNA barcoding in species identifi-cation. Although developing a complete DNA barcode reference library for Nigerianichthyofauna will facilitate species identification and diversity studies, taxonomic re-visions of DNA sequences submitted in databases alongside voucher specimens arenecessary for a reliable taxonomic and diversity inventory.