Abstract: Chlorophyll is the main pigment for photosynthesis of green plants such as crops, and has an important influence on the formation of soybean yield. In this study, the 196 natural populations consisting of domestic and foreign varieties that had been re-sequenced were used as test materials,and the chlorophyll content of seedlings in this population was measured, and the chlorophyll content of seedling stage in this population was determined, and a genome wide association analysis was performed with a mixed linear model. The results showed that 37 significantly related SNP loci were screened according to the threshold, which were located on chromosomes 2, 3, 4, 7, 10, 13 and 16, and 194related genes were searched in the interval of 100 kb upstream and 100 kb downstream of the SNP loci.The 11 candidate genes that might be related to chlorophyll content were screened by GO functional enrichment analysis, KEGG metabolic pathway enrichment analysis and gene function annotation. Four genes related to chlorophyll content in soybean, Glyma.02G185300, Glyma.03G085000, Glyma.10G259900, Glyma.16G037100,were identified by relative expression analysis. The results of this study provide a theoretical reference to investigate the genetic mechanism of chlorophyll content in soybean.