Germ cells transfer genetic materials from one generation to the next, which ensures the continuation of the species. Spermatogenesis, the process of male germ cell production, is one of the most productive systems in adult tissues. This high productivity depends on the well-coordinated differentiation cascade in spermatogonia, occurring via their synchronized cell division and proliferation. Spermatogonial stem cells (SSCs) are responsible for maintaining the spermatogonial population via self-renewal and the continuous generation of committed progenitor cells that differentiate into spermatozoa. Like other stem cells in the body, SSCs are defined by their self-renewal and differentiation abilities. A functional transplantation assay, in which these biological properties of SSCs can be quantitatively evaluated, was developed using mice, and the cell surface characteristics and intracellular marker gene expression of murine SSCs were successfully determined. Another approach to elucidate SSC identity is a cell lineage-tracing experiment using transgenic mice, which can track the SSC behavior in the testes. Recent studies using both these experimental approaches have revealed that the SSC identity changed depending upon the developmental, homeostatic, and regenerative circumstances. In addition, single-cell transcriptomic analyses have further indicated the instability of marker gene expression in SSCs. More studies are needed to unify the results of the determination of SSC identity based on the functional properties and accumulating transcriptomic data of SSCs, to elucidate the functional interaction between SSC behavior and gene products and illustrate the conserved features of SSCs amidst their heterogeneity. Furthermore, the deterministic roles of distinct SSC niches under different physiological conditions in the SSC heterogeneity and its causal regulators must also be clarified in future studies.