Proper immune reconstitution after hematopoietic stem cell (HSC) transplantation requires de novo T cell development in the thymus to ensure a broad and diverse T cell receptor (TCR) repertoire. The clonal relationship between HSCs and T lymphocytes has long been unclear, especially for human T cells. Previous work showed severe clonal restriction in the thymus. Using a cellular barcoding system, which allows quantitative tracking of the progeny of individual stem cells, we here show that clonal restriction is less severe in B cells and that B cells and T cells often arise from different stem cell clones. Finally, when using total CD34+ progenitor cells rather than stem cells, there is a significant contribution from non-stem cell clones to the T cell pool. Thus, relatively short-lived T cell progenitors can provide significant contribution to long living T lymphocytes.