© Springer Nature Switzerland AG 2018. The majority of leukemia patients achieving remission ultimately relapse. Persistence of leukemia stem cells (LSC) capable of regenerating leukemia is a major cause of relapse. There is a pressing need to better understand mechanisms of LSC regulation and their resistance to therapy in order to improve outcomes for leukemia. Chronic myelogenous leukemia (CML) is a lethal myeloproliferative disorder that that is caused by hematopoietic stem cell (HSC) transformation by the BCR-ABL tyrosine kinase. Treatment with tyrosine kinase inhibitors (TKI) has revolutionized CML treatment, but fails to eliminate LSC responsible for propagating and regenerating leukemia. Therefore, patients require continued treatment to prevent relapse. Leukemic and normal stem cells share properties of quiescence and self-renewal, that are supported by bone marrow niches. Persistence of LSC after TKI treatment is related to tyrosine kinase independent mechanisms which include intrinsic properties of LSCs determined by epigenetic alterations, altered transcriptional regulatory networks or mitochondrial/metabolic changes. In addition to cell intrinsic changes, signals from the bone marrow microenvironment (BMM) play a critical role in protecting LSC from TKI treatment. Each type of alteration may offer potential points of intervention for therapeutic targeting of LSC.