Seed hardness and calcium content are important traits for food grade soybean [Glycine max (L) Merr.]. Seed hardness affects water absorption and texture of soyfood products.  Also, calcium in the seed coat negatively correlated with water absorption and seed hardness. Molecular markers linked to quantitative trait loci (QTL) for aforementioned traits will facilitate the process of selecting breeding lines with desired calcium content and seed hardness. The objective of this study was to identify and confirm SSR markers and QTL for calcium content and seed hardness. A total of 125 F _2:4  and F_2:5 lines that were derived from KS4303sp (low calcium and soft seed) x PI 407818B (high calcium and hard seed) cross were grown in two locations (Fayetteville and Keiser, AR) with two replications in 2008 and 2009. Phenotypic results indicated a normal distribution of calcium content and seed hardness in the population. Markers Satt377 and Sat_377 in linkage group (LG) A2, Satt254 and Satt342 in LG D1a, Sat_174 and Sat_268 in LG I, and Sat_224 and Satt547 in LG J were significantly associated with calcium content. Markers Sat_170, Satt330, and Satt292 in LG I were significantly associated with seed hardness. A new QTL was found in LG J near markers Satt547 and Satt414. The molecular markers and QTL that were identified in this research can be used in marker assisted breeding for desired seed calcium content and hardness.