For more than a decade now, the regulatory T (Treg) cell has widely been considered as a critical subpopulation of T cells which can suppress effector T cell responses as well as suppressing the activity of other immune cells, such as mast cell, dendritic cells, and B cells. Treg cells have been broadly characterized as comprising of two main populations: thymus-derived natural Treg (nTreg) cells, and peripherally generated induced Treg (iTreg) cells. Both subsets have similar phenotypic characteristics and comparable suppressive function against T cell-mediated immune response and diseases. However, both Foxp3 positive Treg subsets exhibit some specific differences such as different mRNA transcripts and protein expression, epigenetic modification, and stability. These subtle differences reinforce the notion that they represent unique and distinct subsets. Accurately distinguishing iTregs from nTregs will help to clarify the biological features and contributions of each Treg subsets in peripheral tolerance, autoimmunity and tumor immunity. One difficult problem is that it has not been possible to distinguish iTregs from nTregs using surface markers until two recent articles were published to address this possibility. This review will focus on very recent advances in using molecular markers to differentiate these Treg subsets.