Pollen abortion is one of the major reasons causing the inter-subspecific F1 hybrid sterility in rice and is due to allelic interaction of F1 pollen sterility genes. The microsporogenesis and microgametogenesis of Taichung 65 and its three F1 hybrids were comparatively studied by using techniques of differential interference contrast microscopy, semi-thin section light microscopy, epifluorescence microscopy and TEM. The results showed that there were differences among the cytological mechanisms of pollen abortion due to allelic interaction at the three F1 pollen sterility loci. The allelic interaction at S-a locus resulted in microspores unable to extend the protoplasm membrane with the enlargement of the microspore at the middle microspore stage and finally producing empty abortive pollen. The allelic interaction at S-b locus caused asynchronous development of microspores at the middle microspore stage producing stainable abortive pollen. The allelic interaction at S-c locus mainly led to the non-dissolution of the generative cell wall and finally caused the hybrid F1 mainly producing stainable abortive pollen. Genotypic identification indicated that the abortive pollen were those with Sj allele.