Salinity is a critical environmental challenge that disrupts rice plants' physiological functions and substantially reduces productivity in salt-affected areas—often causing significant yield losses through disruptions in water balance, photosynthesis, and oxidative stability. This study evaluated seven rice parental genotypes and their 21 F₁ hybrids, derived from a half-diallel mating design, under normal and saline conditions to identify key physiological and biochemical traits associated with salt tolerance and to assess genetic diversity using inter-retrotransposon amplified polymorphism (IRAP) markers. The experiment was conducted in 2023 at the Rice Research and Training Center (RRTC). Salinity markedly reduced photosynthetic rate, stomatal conductance, transpiration, relative water content (RWC), and maximum quantum efficiency of photosystem II (Fv/Fm), while increasing membrane permeability, hydrogen peroxide (H₂O₂), and malondialdehyde (MDA) levels. Conversely, antioxidant enzyme activities (SOD, APX, and CAT), proline, and total phenolic contents significantly increased under salinity, with considerable variation among genotypes. Correlation and principal component analyses (PCA) revealed strong positive associations of grain yield with RWC, photosynthetic rate, transpiration, Fv/Fm, SOD, and APX, and negative correlations with oxidative stress indicators (MDA, H₂O₂, and membrane permeability). Crosses P2 × P6 and P5 × P6 clustered closely with traits linked to yield and stress tolerance, followed by P6 × P7 and P5 × P7, indicating superior adaptability to salinity. The IRAP marker analysis revealed 39.7% polymorphism, effectively differentiating the genotypes and confirming substantial genetic diversity valuable for breeding. Overall, maintaining stable water status, photosynthetic efficiency, and robust antioxidant defense mechanisms are key determinants of yield stability under salinity. |