Current study identified the rohu–catla intergeneric hybrids produced from reciprocal crosses at fingerling stage and attempted to find relationship with parent species, Catla (Labeo catla) and rohu (Labeo rohita) through traditional morphological and meristic approaches and a genetic marker, cytochrome C Oxidase I (CO1). Phenotypically, both hybrids (RC, L. rohita♀, and CR, L. catla♀) were intermediate in most of the traits, while some traits resemble their mother species. For accurate identification and phylogenetic relationship of all cross‐types (RR, CC, CR and RC), DNA barcoding by mitochondria COX 1 was also conducted. The constructed Neighbour‐Joining (NJ) tree (K2P) based on COI gene sequence analysis categorized all four crosses into two genetically distant groups. Each hybrid showed an identical phylogenetic relationship with the mother species, that is CR hybrids showed the minimum distance with L. catla, and RC hybrid showed the minimum distance with L. rohita. Moreover, the genetic distance between L. catla and RC hybrid was higher than between L. rohita and RC hybrid.