This review offers an in-depth analysis of mitochondrial DNA (mtDNA) mutations in colorectal cancer stem cells (CSCs), emphasizing their significant impact on tumor dynamics and potential therapeutic strategies. CSCs are a special subpopulation due to their unique capabilities for self-renewal, differentiation, and resistance to conventional therapies. Given that CSCs significantly differ from other tumor cell subpopulations, particularly in their metabolic properties, and considering that colorectal cancer is a malignancy characterized by mitochondrial dysfunction, this review aims to put together existing data on the differences in the mitochondrial genome of CSCs compared to other colorectal tumor cell subpopulations. Additionally, the review seeks to explore the potential roles of these differences and to identify new ideas for therapeutic strategies. Key topics include the identification and properties of CSCs in colorectal cancer, the distinctive features of the mitochondrial genome, and the functional consequences of mtDNA mutations. The review hypothesizes that CSCs rely on well-functioning mitochondria for crucial aspects like energy production; yet, mtDNA mutations can lead to mitochondrial dysfunction, altering CSC characteristics and influencing cancer progression. The article discusses emerging therapeutic approaches targeting mitochondrial function in colorectal CSCs and highlights the need for advanced research, including the development of preclinical models and exploration of targeted therapies, to improve the understanding and treatment of colorectal cancer.