In this study, SSR markers were mainly selected based on the previous linkage analysis related to important agronomic traits, particularly phenological traits. Nine of the 11 significant SSR markers found in this study were previously reported to be linked to flowering time and maturity. Several SNPs identified in the present study were located in or adjacent to the previously reported QTLs (Table 2). Two clusters of significant markers in Gm11 (10 Mb-17 Mb) and Gm11 (33 Mb-36 Mb) were significantly associated with flowering time. Gm11 (10 Mb-17 Mb) contained two flowering time related QTLs [55, 56] and two maturity QTLs , this region was also reported to be linked to flowering time in an association population . The cluster of significant markers on Gm19 (46 Mb-48 Mb) was consistently identified to be closely linked to soybean flowering time through linkage mapping and related to maturity and plant height through association mapping  (Table 3). The cluster of significant markers on Gm20 (43 Mb-44 Mb) identified the same genomic region of flower number QTLs. The markers in those regions could potentially be used by soybean breeders to improve soybean adaptability. Additionally, 35 novel loci associated with soybean flowering time were identified.