Hybridization between Clarias gariepinus and Heterobranchus species (heteroclarias) is deeply embedded in Nigerian catfish aquaculture for the faster growth, and higher survival farmers associate with hybrids, but its widespread, often uncontrolled use raises concerns for the genetic integrity of pure strains and wild populations. This study surveyed 375 catfish farmers and hatchery operators across Rivers State, Nigeria, analyzing data with descriptive statistics, chi-square tests, ANOVA with Tukey post-hoc comparisons, paired and independent t-tests, correlation, multiple linear regression, and binary logistic regression. Hybridization was practiced by 71.5% of farmers, most commonly C. gariepinus female × H. longifilis male (39.5%), and was significantly more frequent among larger-scale and experienced operators (p < 0.001). Only 22.9% of farmers scored "high" on genetic knowledge. Farmers rated hybrids as significantly outperforming pure strains in growth (4.21 vs. 2.87), survival (3.68 vs. 3.12), feed conversion (3.52 vs. 3.18), and market preference (3.89 vs. 3.05; all p < 0.001, d = 0.31–1.42), with no significant difference in disease resistance though these are self-reported ratings, not measured production data. Genetic risk perception correlated positively with years of hybridizing (r = 0.312) and negatively with knowledge (r = –0.287, both p < 0.001). Unavailability of certified pure broodstock (76.5%) and high broodstock cost (64.3%) were the leading constraints; small-scale farms, low knowledge, and no extension contact significantly predicted severe broodstock constraints (Nagelkerke R² = 0.28). The findings support structured broodstock certification, genetic monitoring, and farmer training to reconcile perceived productivity benefits with conservation of Nigeria's catfish genetic resources.