Hybridization is the mating of genetically differentiated individuals or groups and may involve crosses within a species or between separate species. Hybridization can be natural or human-mediated. Reproductive barriers prevent excessive introgression in the former, whereas more often introgression and genetic pollution happen in the latter. Hybridization is more widespread among members of Cyprinidae than any other groups of freshwater fishes. In many carp hatcheries in India, breeders of catla (Catla catla) and rohu (Labeo rohita) are kept in the same tank for breeding, resulting in production of hybrid seeds. Fish hybrids can pose a serious threat to the aquatic environment biodiversity. Consequently, genetic monitoring of organisms is entailed to unambiguously identify parental species and their hybrids. Adopting a multiplex PCR using β-actin gene primers, a kit has been developed to distinguish between the hybrids from their parental species. Agarose electrophoresis revealed one band of about 100 bp in size specific for rohu, another at 300 bp specific for catla, and both bands in hybrid. The kit was tested successfully with the samples collected from many hatcheries located in four Indian states. The rohu-catla early hybrid identification PCR kit could serve as a stepping stone for carp seed certification and hatchery accreditation.