Monitoring the fate of individual cell clones is an important task to better understand normal tissue regeneration, e.g. after hematopoietic stem cell (HSC) transplantation, but also cancerogenesis. Based on their integration into the host cell's genome, retroviral vectors are commonly used to stably mark target cells and their progeny. The development of genetic barcoding techniques has opened new possibilities to determine clonal composition and dynamics in great detail. We recently introduced a modular genetic barcode consisting of 32 variable positions (BC32) with a customized backbone and demonstrated its advantages with regard to barcode calling and quantification. We here applied the BC32 system in a complex in-vivo situation, namely to analyze clonal reconstitution dynamics for HSC grafts consisting of up to three cell populations distinguishable barcoded using different alpha- and lentiviral vectors. In a competitive transplantation setup we were able to follow the differently marked cell populations within individual animals. This enabled us to identify the clonal contribution of the different BC32 constructs during reconstitution and long-term hematopoiesis in the peripheral blood and the spatial distribution in bone marrow and spleen. Thus, we demonstrated, that the system allows tracking the output of individually marked cells in vivo and analyzing their influence on clonal dynamics. Successful application of the BC32 system in a complex, competitive in-vivo situation provided proof of principle that its high complexity and the large Hamming distance between individual barcodes combined with the easy customization facilitate efficient and precise quantification, even without prior knowledge of individual barcode sequences. Importantly, simultaneous high-sensitivity analyses of different cell populations in single animals may significantly reduce numbers of animals required to investigate specific scientific questions in accordance with RRR principles. We conclude that our BC32 system will be excellently suited for various research applications in regenerative medicine and cancer biology.