Stem cells have emerged as a promising source of cell-based therapy in regenerative medicine with several stem cell-based products currently in clinical trials. Despite the immense therapeutic potential, their isolation from some of the emerging sources and their characterization has been naïve owing to the lack of standard markers for the same. Some biomarkers have now been well established for the isolation and characterization of stem cells. However, there are emerging markers that can be used in addition to these conventional markers or independent of them to establish the identity of the stem cells. In this review, an attempt has been made to describe a few conventionally used markers and emerging markers for the identification, isolation and characterization of stem cells from various niches across the three germ layer origins.