Cellular uptake of nanoparticles for stem cell labeling and tracking is a critical technique for biomedical therapeutic applications. However, current techniques suffer from low intracellular labeling efficiency and cytotoxic effects, which has led to great interest in the development of a new labeling strategy. Using silica-coated nanoparticles conjugated with rhodamine B isothiocyanate (RITC) (SR), we tested the cellular uptake efficiency, biocompatibility, proliferation or differentiation ability with murine bone marrow derived hematopoietic stem/progenitor cells. The bone marrow hematopoietic cells showed efficient uptake with SR with dose or time dependent manner and also provided a higher uptake on hematopoietic stem/progenitor cells. Biocompatibility tests revealed that the SR had no deleterious effects on cell cytotoxicity, proliferation, or multi-differentiation capacities in vitro and in vivo. SR nanoparticles are advantageous over traditional labeling techniques as they possess a high level of cellular internalization without limiting the biofunctionality of the cells. Therefore, SR provides a useful alternative for gene or drug delivery into hematopoietic stem/progenitor cells for basic research and clinical applications.