The aim of this study was to investigate the impacts of fluorescent superparamagnetic iron oxide particles (Molday ION Rhodamine B, MIRB) on bioactivities and osteogenetic differentiation of rat bone marrow mesenchymal stem cells (BMSCs). The Cell Counting Kit-8 (CCK-8) method was used to detect the proliferation of superparamagnetic iron oxide (SPIO)-labeled BMSCs and observed the distribution of MIRB in cells; real time -polymerase chain reaction (RT-PCR) method was used to analyze the expressions of such osteogenesis-related genes as bone sialoprotein, alkaline phosphatase (ALP), RUNX2, bonemorphogeneticprotein-2 (BMP-2), type 1 collagen (COL-1) and type 3 collagen (COL-3); ALP-Alizarin red staining and poly-biochemical analyzer were used to qualitatively and quantitatively analyze the osteogenetic metabolites. The labeled MIRB particles distributed in the cytoplasm of BMSCs, the diameter of larger particles could be up to several hundred nanometers, and concentrated around the nuclei, the particles far away from the nuclei were smaller, but the labeled-cells' skeletons and adherent morphology did not change significantly; under the concentration of 25 μg Fe/mL of, MIRB did not affect cellular viabilities of BMSCs, but the gene expressions of bone sialoprotein, ALP, RUNX2 and BMP-2 were decreased, and the secretion amount of ALP and osteocalcin were also declined. MIRB would not affect the proliferation and cell structures of BMSCs, but the SPIO particles aggregated and formed larger granules around the nuclei, which might affect the osteogenesis of BMSCs.