The PEBP gene family encodes proteins with similarity to Phosphatidylethanolamine binding Proteins which found across the animals, plants and microbes. The PEBP genes have important roles in regulation of flowering time and seed dormancy. We presented here a systematic analysis of the PEBP gene family in soybean (Glycine max). At the level of genome-wide screening, we identified 27 PEBP candidate genes from soybean and considered 16 genes with full length of coding sequence as GmPEBP genes. Squence analysis showed the GmPEBP genes had conserved genomic structures and were distributed on nine soybean chromosomes. Genomic structures and chromosome locations were determined for the 16 GmPEBP genes. Phylogenetic analysis grouped the GmPEBP family into three subfamilies, namely FT-like, TFL1-like and MFT-like, and suggested that species-specific expansion contributed to the evolution of this family. Analysis of synonymous substitution rates indicated most duplicated pairs were from the whole genome duplication occurred at 59 and 13 million years ago.