A total of six TGMS (thermosensitive genic male sterile lines) and nine pollinator lines were subjected to molecular characterization using 48 genome-wide SSR (simple sequence repeat) markers. Cluster analysis revealed clear differentiation among the TGMS lines according to their source of origin. The SSR-based genetic distance between the hybrids of the parental lines ranged from 0.36 to 0.79 suggesting a high degree of genetic divergence. Among a set of 54 hybrids generated using parental lines, 32 showed better parent heterosis (+21.7%) while 19 showed mid-parent heterosis (+15.0%). For the trait yield per plant genetic distance (GD) was negatively correlated with $F_1$ performance (r = -0.202), mid-parent heterosis (r = $-0.325^*$; P < 0.05), and better parent heterosis (r = -0.261), while it was positively correlated with specific combining ability (r = 0.042). Based on the grouped genetic distance (GGD), the hybrid combinations were divided into four groups. The GGD showed linear correlation with hybrid performance within the group (GGD = 40 - 50: r = -0.07; GGD = 70 - 80: r = 0.32). This information can be utilized in the development of higher yielding, two-line rice hybrids through selection of intermediately diverse parental lines using GGD.