Objectives Mesenchymal stem cells (MSCs) are promising therapies in dentistry due to their multipotent properties. Selecting donor MSCs is crucial because beagle dogs (canines) commonly used in pre-clinical studies have shown variable outcomes and it is unclear whether canine MSCs (cMSCs) are skeletal site-specific. This study tested whether jaw and long bone cMSCs have disparate in vitro and in vivo multilineage differentiation capabilities. Study Design Primary cMSCs were isolated from mandible (M-cMSCs) and femur (F-cMSCs) of four healthy Beagle dogs. Femur served as non-oral control. Clonogenic and proliferative abilities were assessed. In vitroosteogenic, chondrogenic, adipogenic and neural multilineage differentiation were correlated with in vivobone regeneration and potential for clinical applications. Results M-cMSCs displayed two-fold increase in clonogenic and proliferative capacities relative to F-cMSCs (p =0.006). M-cMSCs in vitro osteogenesis based on alkaline phosphatase (p =0.04), bone sialoprotein (p =0.05), and osteocalcin (p =0.03), as well as adipogenesis (p =0.007), and chondrogenesis (p =0.009) were relatively higher and correlated with enhanced M-cMSC bone regenerative capacity. Neural expression markers, nestin and βIII-tubulin were not significantly different. Conclusions The enhanced differentiation and bone regenerative capacity of mandible MSCs may make them favorable donor graft materials for site-specific jaw bone regeneration.