The two cultivated rice species, Oryza sativa and Oryza glaberrima, are morphologically alike but are reproductively isolated from each other by hybrid sterility. The hybrid is male sterile but partially female fertile. Backcross experiments were conducted to introduce an alien factor controlling hybrid sterility from O. glaberrima (W025) into O. sativa (T65wx) and examine the genetic basis. An extracted sterility factor, closely linked to the wx locus, induced gametic abortion due to allelic interaction and was tentatively designated as S(t). The segregation patterns for infertility was explained by assuming that W025 and T65wx carried S(t) and S(t)a, respectively, and gametes with S(t)a aborted only in the heterozygote (S(t)/S(t)a) although the elimination of female gametes was incomplete. Thus, S(t) seemed to be intermediate between a gamete eliminator and pollen killer. However, S(t) was proven to be likely the same as S1 which was formerly reported as gamete eliminator in a different genetic background of O. sativa. In addition, a chromosomal segment containing S1 (or S(t] caused a marked suppression of crossing over around it, suggesting the presence of an inversion. Further, female transmission of S1a increased as the segment containing S1 became small by recombination. After S1 was further purified by successive backcrosses up to the BC15 generation, it became pollen killer. The present results give evidence that a profound sterility gene such as gamete eliminator can be made from accumulation of pollen killer and its modifier(s) when pollen killer and modifier(s) are linked, they behave as a gene complex in the hybrid.