Hybridization and speciation are critical processes influencing biodiversity and ecosystem dynamics, particularly in regions rich in aquatic biodiversity such as India. This study investigates the role of hybridization in the adaptive radiation and speciation of Indian major carps, specifically Catla (Catla catla), Rohu (Labeo rohita), and Mrigal (Cirrhinus mrigala). Through comprehensive genetic analysis using molecular markers, we assess the genetic diversity and hybridization patterns among these species across various habitats in India. Our findings reveal significant genetic differentiation and hybridization events that contribute to the genetic richness of these populations. Ecological assessments indicate that hybrid carps occupy unique ecological niches, demonstrating distinct adaptive traits compared to their parent species. The implications of hybridization for aquaculture practices are profound, suggesting both opportunities and challenges for sustainable fish farming. This research highlights the need for integrated conservation and aquaculture management strategies to preserve genetic diversity and enhance the productivity of fish aquaculture in India. By understanding the dynamics of hybridization and speciation, we can better protect biodiversity and optimize aquaculture practices for future sustainability.