In this study, a total of 85 apple polygalacturonase genes were characterized and clustered into seven groups based on the Malus × domestica whole-genome sequence. These genes coded for proteins containing 176–1 125 amino acids with isoelectric points ranging from 4.68 to 9.58.The predicted Md PG genes were distributed on all chromosomes except the 14 th. We then systematically analyzed conserved Md PG protein motifs and the structures of Md PG genes. We identified Md PG proteins containing four conserved motifs that are widely found in different PG proteins.Additionally, we found that Md PG75 was the largest gene, encompassing 18 exons. Finally, we systematically analyzed the functional connection network of Md PG proteins and predicted the functions of related Md PG genes before undertaking a preliminary validation. Overall, we have described the genome-wide identification and analysis of the apple PG gene family. In this study, a total of 85 apple polygalacturonase genes were characterized and clustered into seven groups based on the Malus × domestica whole-genome sequence. These genes coded for proteins containing 176-1 125 amino acids with isoelectric points ranging from 4.68 to 9.58. The predicted Md PG genes were distributed on all chromosomes except the 14 th. We then systematically analyzed the conserved Md PG protein motifs and the structures of Md PG genes. We identified Md PG proteins containing four conserved motifs that are widely found in different PG proteins. Finally, we systematically analyzed the functional connection network of Md PG proteins and predicted the functions of related Md PG genes before undertaking a preliminary validation. Overall, we have described the genome-wide identification and analysis of the apple PG gene family.