To determine in the baboon model the identities and functional characteristics of endothelial progenitor cells (EPCs) mobilized in response to artery ligation, we collected peripheral blood mononuclear cells (PBMNCs) before and 3 days after a segment of femoral artery was removed. Our goal was to find EPC subpopulations with highly regenerative capacity. We identified 12 subpopulations of putative EPCs that were altered >1.75-fold; two subpopulations (CD146+/CD54–/CD45– at 6.63-fold, and CD146+/UEA-1–/CD45– at 12.21-fold) were dramatically elevated. To investigate the regenerative capacity of putative EPCs, we devised a new assay that maximally resembled their in vivo scenario, we purified CD34+ and CD146+ cells and co-cultured them with basal and mobilized PBMNCs; both cell types took up Dil-LDL, but purified CD146+ cells exhibited accelerated differentiation by increasing expression of CD31 and CD144, and by exhibiting more active cord-like structure formation by comparison to the CD34+ subpopulation in a co-culture with mobilized PBMNCs. We demonstrate that ischaemia due to vascular ligation mobilizes multiple types of cells with distinct roles. Baboon CD146+ cells exhibit higher reparative capacity than CD34+ cells, and thus are a potential source for therapeutic application.