Purple acid phosphatases (PAPs) are members of the metallo-phosphoesterase family and have been known for their important roles in P acquisition and recycling in plants.Low phosphorus (P) availability is a major constraint to soybean (Glycine max (L.) Merr) growth and production.Comparative studies on the structure, transcriptional regulation and response to phosphate (Pi) deprivation of the soybean PAP gene family would facilitate further insights into the potential physiological roles of GmPAPs.In the present study, 35 PAP genes were identified from soybean genomes, which can be classified into three distinct groups including six subgroups in the phylogenetic tree.The expression pattern analysis showed flowers possessed the largest number of tissue-specific GmPAP genes under normal P conditions.The expression of 23 GmPAPs was induced or enhanced by Pi starvation in different tissues.