Abstract
DNA barcoding provides an efficient molecular approach for species identification using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences. This study aimed to generate DNA barcodes for endangered freshwater fish species of Bangladesh and evaluate their taxonomic identification. A total of 12 species were successfully identified with 98–100% sequence similarity using GenBank and BOLD databases, confirming the reliability of COI for species-level discrimination. The amplified sequences exceeded 650 base pairs, ensuring high-quality mitochondrial DNA analysis. However, slight discrepancies were observed in certain species, such as Osteobrama cotio and Botia dario, which showed relatively lower identity scores (~98%). Notably, COI sequences of Channa striata and Glossogobius sexualis were absent in the BOLD database but were recorded in GenBank, highlighting gaps in global reference databases and contributing new sequence data through this study. The findings also emphasize challenges related to database inaccuracies and taxonomic ambiguities. Phylogenetic analysis further validated species identification and revealed the dominance of Cypriniformes, consistent with regional biodiversity patterns. Additionally, variations in species composition compared to previous studies suggest the influence of environmental changes and sampling strategies. Overall, this study demonstrates the effectiveness of DNA barcoding as a reliable tool for fish identification and biodiversity assessment, contributing valuable genetic resources for conservation and management of freshwater fish species in Bangladesh.