Abstract: Forty-eight PG genes were classified into three major clades by phylogenetic analysis and each clade contained PG genes that involved in fruit softening. PG genes belonged to clade A and clade B had functional divergence obviously. There were some different amino acid sites in amino acid sequence of PG genes from different clades. PG genes in clade A and clade C had a deletion of 60–70 amino acids in N terminal end compared with PG genes in clade B. Variation in the structure of PG genes（mainly including promoter regions，introns and encoding regions）had a significant impact on their functions. PG genes in apple and peach were accurately localized in genome respectively and around the genes there were some fruit softening markers.

Key words: polygalacturonase genes, fruit softening, phylogenetic analysis, genomic localization