High temperatures during seed fill, coupled with alternating periods of wet and dry conditions, can cause seed deterioration in soybean by promoting seed coat wrinkling and seed shriveling. This can predispose the seeds to mechanical damage at harvest and further reduce germinability. This has become a production problem in the mid-southern United States, where the early soybean production system (ESPS) is widely used. Previous studies identified a single recessive gene (Shr) in T-311, located on linkage group F, which causes seed shriveling. This study was undertaken to identify and genetically map new gene(s) that affect seed coat wrinkling in soybean. Crosses were made between a smooth-seeded accession (PI 567743) and a wrinkled-seeded accession (PI 87623). The P1, P2, F1, F2, and BC1 generations were phenotyped for seed coat wrinkling in a greenhouse in Stoneville, MS during the summer of 2006. Genetic analysis suggested that the wrinkled seed trait in PI 87623 was inherited as a single recessive gene, and that this gene is different from the Shr gene in T-311. A linkage map was developed using 195 SSR and SNP markers on 168 F2 individuals of the cross PI 567743 x PI 87623. QTL analysis identified only one significant locus on linkage group A1, a different chromosomal location from the Shr gene, confirming identification of a new gene that controls seed coat wrinkling in soybean. This information will assist plant breeders in developing cultivars with improved seed quality for heat stressed production environments such as the ESPS.