Reproductive barriers often arise in hybrid progeny between two varietal groups of Asian cultivated rice ( Oryza sativa L.), Japonica and Indica. Hybrid breakdown showing poor growth habit, and complete sterility was found in the backcrossed progeny derived from a cross between a Japonica variety, Asominori, and an Indica variety, IR24. We employed RFLP analysis in the segregating population to study the genetic basis underlying hybrid breakdown. It was found that the hybrid breakdown is caused by a set of two nuclear genes, which were symbolized as hwe1 and hwe2. The parental varieties, Asominori and IR24, carry hwe1(+) hwe1(+) hwe2hwe2 and hwe1hwe1hwe2(+) hwe2(+) genotypes, respectively, whereas the progenies that showed a weakness performance carry the double recessive genotype ( hwe1hwe1hwe2hwe2). Abnormality was not observed in the progenies that carry the other genotypes, indicating that a single dominant allele at either locus is necessary for normal growth. Based on linkage analysis with RFLP markers, the hwe1 locus was located between RFLP markers R1869 and S1437 on chromosome 12 and the hwe2 locus was located between R3192 and C1211 on chromosome 1. The genetic basis was reconfirmed using near-isogenic lines carrying the genes with reciprocal genetic backgrounds. The present study provides clear evidence, viewed by previous workers, that hybrid breakdown is attributed to complementary genes from both parents.