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Factors that govern the complex formation of memory T cells are not completely understood. A better understanding of the development of memory T cell heterogeneity is however required to enhance vaccination and immunotherapy approaches. Here we examined the impact of pathogen- and tissue-specific cues on memory CD8 + T cell heterogeneity using high-dimensional single-cell mass cytometry and a tailored bioinformatics pipeline. We identified distinct populations of pathogen-specific CD8 + T cells that uniquely connected to a specific pathogen or associated to multiple types of acute and persistent infections. In addition, the tissue environment shaped the memory CD8 + T cell heterogeneity, albeit to a lesser extent than infection. The programming of memory CD8 + T cell differentiation during acute infection is eventually superseded by persistent infection. Thus, the plethora of distinct memory CD8 + T cell subsets that arise upon infection is dominantly sculpted by the pathogen-specific cues and further shaped by the tissue environment., Competing Interests: The authors declare no competing interests., (© 2020 The Author(s).)