Phospholipase D (PLD) and its product phosphatidic acid play important roles in the regulation of plant growth, development, and stress responses. The genome database analysis has revealed PLD family in Arabidopsis, rice, poplar and grape. In this study, we report a genomic analysis of 18 putative soybean (Glycine max) PLD genes (GmPLDs), which exist in the 14 of 20 chromosomes. GmPLDs were grouped into six types, α(3), β(4), γ, δ(5), ε(2), and ζ(3), based on gene architectures, protein domains, evolutionary relationship, and sequence identity. These GmPLDs contained two HKD domains, PX/PH domains (for GmPLDζs), and C2 domain (for the other GmPLDs). The expression patterns analyzed by quantitative reverse transcription PCR demonstrated that GmPLDs were expressed differentially in various tissues. GmPLDα1, α2, and β2 were highly expressed in most tissues, whereas GmPLDδ5 was only expressed in flowers and GmPLDζ1 was predominantly expressed in flowers and early pods. The expression of GmPLDα1 and α2 was increased and that of GmPLDγ was decreased by salt stress. GmPLDα1 protein expressed in E. coli was active under the reaction conditions for both PLDα and PLDδ, hydrolyzing the common membrane phospholipids phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. The genomic analysis for soybean PLD family provides valuable data for further identity and characterization of their functions.