Sucrose is a desirable sugar in soybean seed that affects the quality and taste of soyfoods, while stachyose is a non-digestible sugar that induces flatulence in non-ruminant animals. Therefore, soybean cultivars with high sucrose and low stachyose would be valuable for soyfoods and meal markets. The objectives of this study were to identify QTL associated with seed sucrose and stachyose content using Simple Sequence Repeat (SSR) markers. MFS-553 (low sucrose) was crossed with PI 243545 (high sucrose), and Osage (normal stachyose) was crossed with V99-5089 (low stachyose) to develop the QTL mapping populations. A total of 626 random SSR primers covering 20 soybean linkage groups (LGs) were used to screen the parents; 209 were polymorphic between MFS-553 and PI 243545 and 201 were polymorphic between Osage and V99-5089. Polymorphic markers were used to screen the F2 populations, and F3 and F5 seeds were analyzed for sucrose and stachyose using High Performance Liquid Chromatography (HPLC). The sucrose content in MFS-553 x PI 243545 cross fitted to a normal distribution whereas stachyose content in Osage x V99-5089 followed a bimodal distribution. Single marker analysis showed that nine SSR markers on LG D2, G, I, K, and L were associated with sucrose content in MFS-553 x PI 243545, among which Satt419 and Satt367 on LG I were close to a previously reported sucrose QTL. Three SSR markers on LG O within a 5 cM region were strongly associated with stachyose content in the Osage x V99-5089 cross, two of which (Sat_282 and Satt173) were also reported in a previous study, indicating a single gene for stachyose content. SSR markers and sugar QTL/genes identified from this study can be used for marker assisted selections in breeding soybean lines with desired sugar profile.