The study evaluated genetic and morphological diversity of two economically significant major carp species namely, Labeo rohita, and Cirrhinus mrigala, inhabiting the River Chenab (Chiniot Pull L1, Trimmu Barrage L2 and Head Muhammad Wala L3) Punjab, Pakistan. Fish specimens were identified structurally, and the mitochondrial COI gene sequence was utilized for genetic analysis. MEGA 11 and the K2P model were used to construct Maximum Likelihood (ML) phylogenetic trees. Using an online QR code generator, QR codes were made for accurate fish identification. With an average length of 664 base pairs (bp), 60 mitochondrial COI barcode sequences were obtained. Transitional mutations were more common than transversions. Each species showed one haplotype (H = 1), haplotype diversity (Hd) = 0.00 and nucleotide diversity (Pi) = 0.00 in the analyzed COI region. In nucleotide composition GC content (45.5%) was lower than the AT content (54.5%). The evolutionary tree showed degree of resemblance in the limit of 99% for sequences of Labeo rohita and Cirrhinus mrigala, which grouped in two clades because they were in the two genera but the same family. In the current study, DNA barcoding has demonstrated that it is a reliable approach for species identification. The molecular data generated in this study provides baseline information on species-level identification and intraspecific genetic variation of the examined carps, which may support future investigations of fish health observation, aquaculture management and fisheries monitoring.

To Cite This Article: Batool A and Jabeen F, 2026. Aquatic animal health management through DNA barcoding and morphological identification of Labeo rohita and Cirrhinus mrigala from the river Chenab, Pakistan. Pak Vet J, 2026, 46(10): 2478-2486. http://dx.doi.org/10.29261/pakvetj/2026.226