Mesenchymal stromal cells (MSCs) are promising tools in regenerative medicine and targeted therapies. Although different origins have been described, there is still huge need to find a valuable source harboring specific subpopulations of MSCs with precise therapeutic functions. Here, we isolated by fluorescence activated cell sorting technique, two populations of Wharton's jelly (WJ)-MSCs based on their aldehyde dehydrogenase (ALDH) activity. Two different ALDH activities (low vs. high) were thus observed. We then analyzed their gene expression profile for stemness, phenotype, response to hypoxia, angiogenesis, hematopoietic support, immunomodulation and multilineage differentiation abilities (osteogenesis, adipogenesis, and chondrogenesis). According to ALDH activity, many differences in the mRNA expression of these populations were noticed. In conclusion, we provide evidences that WJ harbors two distinct populations of MSCs with different ALDH activity. These populations seem to display specific functional competences that may be interesting for concise therapeutic applications.