Percentage of exserted stigmas (PES) was investigated in Hainan by using a population of 127 DH population derived from a cross between a high-PES indica variety Zaiyeqing 8 (ZYQ 8) and a low-PES japonica variety Jingxi 17(JX 17) and its molecular linkage map of 234 markers. Two QTLs (qPES-2, qPES-3) for PES were located on chromosome 2 and 3, respectively. There is no difference between the QTLs for single stigma exsertation and total PES, but the only QTL for dual stigma exsertation located on chromosome 2, whose positive additive effect was from ZYQ 8. Simultaneously the detected QTLs for spikelets per panicle located on chromosome 6,8, respectively and had no linkage relation with the QTLs for PES.