Bone marrow transplantation is of increasing utility in cancer treatment and is an important component of gene therapy protocols. Understanding the functional identities of progenitor cells involved in repopulation is important for the optimal application of this procedure. We have simultaneously used two types of genetic markers to study engraftment of mice after irradiation. The first involves intrinsic genetic differences, including a cellular marker, between two mouse strains used to construct chimeric mice by aggregating embryos. To produce a second marking system, bone marrow from these allophenic mice was subsequently infected with retrovirus. Individual progenitor cells, including primitive lympho-hematopoietic stem cells, participating in repopulation were identified by virtue of their uniquely marked clonal progeny. In this way numbers and genotypic identities of clones contributing to repopulation were determined. Engraftment could be divided into two distinguishable temporal phases. The first comprised roughly the first 3-4 months following transplant and was characterized by numerous clones, many of which apparently had limited lineage potencies. The subsequent phase was characterized by few, often a single, clones represented in all lympho-hematopoietic tissues. These findings are consistent with the notion that different classes of progenitor cells are differentially responsible for temporal progression. More differentiated, perhaps lineage restricted, progenitors transiently dominate the first few months before the emergence of pluripotent stem cell clones. Senescence of progenitors of the first phase may reflect their limited lifespans. A clear genotypic difference was obvious in engraftment. Cells of one strain, DBA/2, completely dominated the first temporal phase, whereas the C57BL/6 partner strain dominated the second phase. The genotype-restricted dominance of different stages of repopulation suggests important differences in the organization and regulation of stem and progenitor cell populations. Inherent differences in seeding, proliferation, and differentiation of progenitors of the two inbred strains may account for the differences. This in vivo model of competitive repopulation provides the opportunity to explore potentially important loci in the process of engraftment. We propose that DBA/2 progenitor cells, due to a proliferative and/or numerical advantage, account for their superiority immediately after engraftment. C57BL/6 stem cells, with long-term repopulating potential, predominate later, perhaps because of subtle numerical or proliferative advantages.