Leukemia stem cells(LSC) are the root causes of the leukemia, and are also the main reason for the leukemia relapse. Researchers hope that there are some methods to specifically mark the LSC and to clear them for promoting the advancements in the treatment of leukemia. This review discusses the biological characteristics of LSC and its microenvironment, the current internationally recognized main methods for specific marking of LSC, including marking LSC self-renewal, apoptosis signaling pathways, microenvironment, cell cycle-related signaling pathways and LSC-specific immune phenotype, so as to eliminate LSC and minimal residual disease through these marking ways. But, at present, there are no specific methods to remove leukaemia stem cells independently, possibly the combination of LSC immune phenotype with blocking the microenvironment signaling pathways can target at and remove LSC, thus improving the prognosis of leukemia.