Mesenchymal progenitors residing in the muscle interstitial space contribute to pathogeneses such as fat infiltration and fibrosis. Because fat infiltration and fibrosis are hallmarks of diseased muscle, it is important to establish an accurate and reproducible method for isolating mesenchymal progenitors for research on muscle diseases. In this chapter, we describe methods based on fluorescence-activated cell sorting (FACS) to purify mesenchymal progenitors from mouse and human skeletal muscle using the most reliable marker for mesenchymal progenitors, PDGFRα. These methods allow concurrent isolation of the muscle stem cells called satellite cells. The quality of isolated mesenchymal progenitors is confirmed by their remarkable adipogenic potential without myogenic capacity, while purified satellite cells possess robust myogenic activity with no adipogenic potential. Simultaneous isolation of both mesenchymal progenitors and satellite cells from mouse and human tissues provides a powerful platform for studying skeletal muscle regeneration and diseases.