The cytological mechanisms of the elite seedless Ponkan accession were systematically studied through comparing with its maternal parent Jiangxi Ponkan and E-gan No.1. Male gamete fertility,self-incompatibility and embryo development were investigated. The results showed that male gamete of Jiangxi seedless Ponkan developed abnormally and the pollen fertility of the elite seedless Ponkan was significantly lower than that of the control. Meanwhile the abnormal meiosis percentage of pollen mother cell was severely higher than that of the control. Morphological and anatomical structure of microspore mother cell of the elite seedless Ponkan was different from that of the control. The seedless Ponkan accession had self-compatibility and its pollen tubes grew downward through the style normally. Embryo abortion occurred at early developmental stage causing the seedlessness of the elite seedless accession. The 3rd week after pollination was the critical period to observe the embryo abortion. Seed numbers in fruit did not change significantly by self-pollination or cross-pollination. Embryo abortion is responsible for the elite seedless Ponkan accession.