Cowpea mild mottle virus (CpMMV) is an important viral pathogen that seriously influences the yield and seed quality of soybeans worldwide. Resistance breeding is one of the most effective, economical, and environmentally safe strategies for controlling the disease caused by CpMMV. However, only few resistance genes have been identified in soybeans. In this study, the resistance of 169 soybean germplasms from Northeast China to a CpMMV strain isolated from soybean in China was evaluated, and a genome-wide association study (GWAS) was then performed to find possible resistance genes in these soybean germplasms. Nine resistant soybean germplasms were identified and two single nucleotide polymorphism sites (SNPs) were found to be closely associated with CpMMV resistance. A total number of 51 and 25 candidate genes neighboring the resistance-associated SNPs on chromosomes 6 and 12, respectively, were identified, among which one receptor-like kinase (RLK) on chromosome 6 and 2 toll-interleukin-1 receptor nucleotide-binding leucine-rich repeat receptors (TNLs) on chromosome 12 were recognized as the most probable resistance genes, respectively. Together, these data provide new insights on the resistance resources of soybeans to CpMMV, which will benefit the breeding of CpMMV-resistant soybean cultivars.