Oryza glaberrima is a valuable and potential source of useful genes of interest for rice improvement. However, hybrid sterility between O. sativa and O. glaberrima is a main reproduction barrier when favourable traits/genes are transferred from O. glaberrima to O. sativa. Understanding of the nature of hybrid sterility is critical and will contribute to overcome this problem. In this study, a new gene from O. glaberrima was mapped as a Mendelian factor controlling hybrid sterility in an advanced backcross population derived from one accession of O. glaberrima as a donor parent and ÔDanjing 5Õ (a japonica cultivar from Liaoning) as recurrent parent. Sterile plants as female parent from F 1 were observed after six backcrosses. The BC 6 F 1 population containing 47 plants was screened with 142 simple sequence repeat (SSR) markers on all 12 chromosomes to analyse the pollen fertility. As a result, one locus qSS-2 on chromosome 2 was distinct from all previously reported ones. A new locus designated as S36(t) was identified and mapped to interval between two SSRs RM208 (0.5 centiMorgans, cM) and RM482 (0.8 cM) on rice chromosome 2.