A locus for male gamete abortion in hybrids for Japonica and Indica rice was identified with the aid of marker genes Rc and Est-9 on chromosome 7. In an Indica-Japonica cross, AKAMAI 1/IR50, the Indica allele Est-9 ² was transmitted via the male gamete with a ratio of 0.29 instead of the normal 0.5, whereas no segregation distortion was observed for the Rc locus. The recombination value (p) for Est-9 and Rc was estimated to be 0.38 by a least square method after adjusting Mendelian segregation ratios with the male transmission ratios of 0.29 (Tr) for Est-9 ² and 0.71 (1-Tr) for Est-9 ¹. The recombination value (q) for the new locus for male gamete abortion, ga-11, and Est-9 was estimated to be 0.23 by using 56 F₃ lines from F₂ plants which were heterozygous for the Est-9 locus. No linkage for Rc and ga-11 was found. Therefore, the two markers and ga-11 were located in the order of ga-11-Est-9-Rc. Using the estimated recombination value (q), the male transmission rate (k) of ga-11 ^a was estimated to be 0.11 with the F₂ data and-0.07 with the F₃ line data. Thus, it was apparent that male gametes possessing ga-11 ^a were frequently aborted in the Indica-Japonica hybrid.