Most of the economically important Chinese pears display S-RNase-based gametophytic self-incompatibility (GSI). By genomic PCR and sequence analysis, five new S-RNase alleles (S5a and S11 to S14) in three Chinese sand pear (Pyrus pyrifolia) cultivars and six (Sa to Sf) in five Chinese white pear (P. bretschneideri) cultivars were identified. Comparison of nucleotide sequences of S-RNase alleles from the two different Chinese pear species revealed that Sa, Sb, and Sd of P. bretschneideri was identical to S8, S14, and S12 of P. pyrifolia, respectively. We obtained the full-length cDNA sequence of S12 and determined S12 was expressed only in the style of pear. The functions of the new S-RNase alleles were confirmed by the controlled pollination tests. As the results, the eight cultivars of the two Chinese pear species were genotyped as: 'Maogong' (S11S12), 'Cangxixueli' (S5aS13), 'Guiguan' (S2S14), 'Jinfeng' (SaSb), 'Matihuang' (SbSc), 'Jinhuasihao' (SdSe), 'Youli' (SbSc), and 'Jitui' (ScSf). Elucidation of S-genotype would contribute to higher and stable yields in the orchards and a more efficient breeding programme of pears.