Germ cells support the continuation and evolution of species. In mammals, the germ line trajectory, originating from a small number of primordial germ cells (PGCs), has been a focal point investigated using mouse models. Yet, the precise contribution of individual PGC lineages to the adult gametes and to the next generation, a process that incubates and transmits de novo genetic mutations and epigenetic variability, remains enigmatic. Here, by employing a Polylox1 DNA barcoding technology and mathematical modelling, we unveiled the clonal dynamics of the mouse male germline from development through adulthood and to the next generation. We found that, within cells initially specified to become germ cells in early embryogenesis, >30% of clones are lost during migration before settling at the testis, with the surviving PGC clones expanded quite unevenly. In contrast, within developing testes, in which PGCs are compartmentalised into quasi-one-dimensional seminiferous tubules, their clonal repertoire (i.e., diversity and size distribution) is preserved until adulthood. Further, the clonal repertoire in spermatogonial stem cells (SSCs) is proportionally mirrored in sperm production and in the offspring. These results advocate that early pruning and late preservation of male germ cell clones underlie the diversity and skewness of cell lineages transmitted to the next generation.