The purpose of this study was to evaluate the use of three different superparamagnetic iron oxide (SPIO) particles for labeling of ovine and equine bone marrow (BM)-derived multipotent stromal cells (MSCs) in vitro. MSCs were obtained from five adult sheep and horses, respectively. After three passages (p3), cells were labeled with either 1) Molday ION Rhodamine B, 2) Endorem, 3) Resovist, or 4) remained unlabeled as control. Labeling efficiency, marker retention, and long-term detectability in MRI until p7 were evaluated. Further, proliferation capacity and trilineage differentiation as indicators for potential impact on stromal cell characteristics were assessed. MSCs of both species were successfully labeled with all three SPIO products. A high, exclusively intracellular, iron uptake was achieved by Molday ION Rhodamine B only. Labeling with Resovist led to prominent extracellular iron presence; labeling with Endorem was less efficient. During MRI, all labeled cells showed strong hypointense signals, contrary to unlabeled controls. Resovist induced the largest areas of hypointense signals, followed by Molday ION Rhodamine B and Endorem. MRI signal detectability decreased from p4 to p7. Proliferation, adipogenic, and osteogenic differentiation potential were not reduced by cell labeling compared to unlabeled cells. Chondrogenic differentiation capacity decreased with increasing amount of iron associated with the cells. Among the three products, Resovist and Molday were identified as promising labeling agents. While Resovist achieved superior results in most of the assessed parameters, Molday ION Rhodamine B ensured intracellular iron uptake without extracellular SPIO complexes and consistent hypointense signals on MRI.