Spermatogonial stem cells (SSCs) are increasingly studied for potential use in tissue regeneration due to their ability to dedifferentiate into embryonic stem cell-like cells. For their successful therapeutic use, these cells must first be expanded in vitro using an appropriate culture system. We hypothesized that a hydrogel with proper biochemical and biomechanical properties may mimic the composition and structure of the native basement membrane onto which SSCs reside, thus allowing us to control SSC proliferation. This hypothesis was examined in two-dimensional (2D) and three-dimensional (3D) cultures using hydrogels formed from calcium cross-linked alginate molecules conjugated with synthetic oligopeptides containing the Arg-Gly-Asp sequence (RGD peptides). The RGD peptide density (N(RGD)) in gel matrices was controlled by mixing alginate molecules modified with RGD peptides and unmodified alginate molecules at varied ratios. The mechanical stiffness was controlled with the cross-linking density of gel matrices. Interestingly, the RGD peptide density modulated cell proliferation in both 2D and 3D cultures as well as the number and size of SSC colonies formed in 3D cultures. In contrast, cell proliferation was minimally influenced by mechanical stiffness in 2D cultures. Overall, the results of this study elucidate an important factor regulating SSC proliferation and also present a bioactive hydrogel that can be used as a 3D synthetic basement membrane. In addition, the results of this study will be broadly useful in controlling the proliferation of various stem cells.