Paired related homeobox 1 (Prrx1) is expressed in mesenchymal progenitors in the limb buds and craniofacial mesenchyme. The mouse lineage tracing study indicates that Prrx1-positive cells enable to produce the chondrocytes, osteoblasts, bone marrow stromal cells, tendon/ligament cells and dermal fibroblasts during the development of limb skeleton. Here we use the single-cell RNA sequencing (scRNA-seq) to dissect the heterogeneity of Prrx1-positive cells and hierarchy of its descendant cells. Limb from each fetal stage (E12.5, E14.5, E16.5) of Prrx1 transgenic GFP mice, in which GFP is expressed under the control of the Prrx1 promoter, were single-celled by collagenase treatment, and then Prrx1-GFP-positive/negative cells were isolated by FACS. These cells were subjected to scRNA-seq by the microwell-cased scRNA-seq technology (BD Rhapsody). We have captured about 20,000 single cells, and identified 20 subpopulations highlighting the heterogeneous nature of the limb development. Our scRNA-seq studies provide a detailed molecular information that patterns limb skeleton.