Chinese cherry (Prunus pseudocerasus L) is an allotetraploid species and exhibits natural self-compatibility However, the full-length cDNA sequences, functional analysis and the transcripts of S-RNase alleles in Chinese cherry cultivars are not known. In the two cultivars Taixiaohongying and Laiyang Short Cherry with S(1)S(2)S(3)S(4) genotypes, two S-RNases were transcribed in Northern blotting, and the two full-length cDNAs of S-RNase were cloned and analyzed. As the result, the transcribed S-RNases were S(1)-RNase and S(2)-RNase The two complete cDNA sequences of S(1)-RNase and S(2)-RNase were registered as EU073938 and EU073939, respectively, and had characteristic structure of rosaceous S-RNases based on their sequences indicating that they had normal function for S-RNase in the style The S(3)-RNase and S(4)-RNase were not transcribed in the style and were nonfunctional for S-RNase, so S(3m) and S(4m) could be used to represent the nonfunctional S(4)-RNase and S(4)-RNase. The phylogenetic analysis implied that the S-RNases of Prunus. including Chinese cherry, had lower intra-specific similarity and diverged earlier than the divergence of species in Prunus