Reproductive isolation is both an indicator of speciation and a mechanism for maintaining species identity. Here we review the progress in studies of hybrid sterility in rice to illustrate the present understanding of the molecular and evolutionary mechanisms underlying reproductive isolation. Findings from molecular characterization of genes controlling hybrid sterility can be summarized with three evolutionary genetic models. The parallel divergence model features duplicated loci generated by genome evolution; in this model, the gametes abort when the two copies of loss-of-function mutants meet in hybrids. In the sequential divergence model, mutations of two linked loci occur sequentially in one lineage, and negative interaction between the ancestral and nascent alleles of different genes causes incompatibility. The parallel-sequential divergence model involves three tightly linked loci, exemplified by a killer-protector system formed of mutations in two steps. We discuss the significance of such findings and their implications for crop improvement.