The discovery of cardiac stem cells (CSCs) able to renew the pool of cardiomyocyte raised the question of how these cells can be recognized and directed towards cardiac reconstruction after severe ischemic injury. The functional studies demonstrated that the differentiation of adult cardiac stem cells reproduce the stages observed in the embryonic development. Each stage is characterized by a complex molecular signature, which can be used for identification and molecular targeting. Three major markers have been used to isolate CSCs: c-kit, Sca-1, and Isl1 and different progenitor populations have been described: side-population (SP), cardiosphere-derived, epicardial-derived. Combinations between the main three markers and other transcription factors, cell surface proteins and regulatory RNAs may delimit even further the cardiac precursors. Accumulation of data leads to the idea that a single, yet unidentified unique cardiac stem cell is at the origin of those observed variants. In this review, we intended to summarize the actual knowledge about the main molecular markers of cardiac stem cells.