While a tree grows over many years, somatic mutations accumulate and generate a genetically diverse individual. Trees can transmit such mutations to subsequent generations, potentially enhancing the genetic diversity of the population. We study a mathematical model to understand the relationship between within-individual genetic variation and branching architecture. We generate branching architecture by repeatedly adding two new branches (main and lateral daughter branches) to each terminal branch (mother branch). Tree shape is determined by two key parameters: daughter-mother ratio (DM) and main-lateral ratio (ML). During branch elongation, somatic mutations accumulate in the stem cells of a shoot apical meristem (SAM) at the tip of each branch. In branching, all the stem cells are passed on from the mother to the main daughter branch, but only one stem cell is chosen for the lateral daughter branch. We evaluate genetic variation by Z, the mean genetic differences between all pairs of branches of a tree, and examine how Z varies with DM and ML while keeping the total branch length constant. As a result, (1) Z attains the maximum for an intermediate DM, when stem cells in the SAM are genetically homogeneous; (2) Z decreases monotonically with DM when stem cells are genetically heterogeneous; and (3) Z increases monotonically with ML. Even though the total branch length remains constant, the within-individual genetic variation differs substantially. The results demonstrate the importance of branching architecture in storing genetic diversity.