The aging of adult stem cells has been researched by the traditional theories and methods of the aging of somatic cells and the unique role of the self-renew and the stem genes of adult stem cells has been ignored by now in the aging of adult stem cells. The down-regulation of stem genes may be the major cause of the aging of stem cells. By analysis of the relevant information, we found that the expression levels of the stem genes and aging-related genes are associated with mutual antagonism which can be reflected in the following four aspects: The aging of stem cells is accompanied by down-regulation of the stem genes; The aging of cells is inhibited by the expression of the stem genes; The stem genes inhibits the expression of aging-related genes; The knockdown of an aging-related gene enhances the expression of the stem genes. The conclusion in this review that the expression levels of the stem genes and aging-related genes are associated with mutual antagonism provides a solid molecular basis of the viewpoint that the aging of adult stem cells may originate from the decline of stemness.