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Neuronal dendrites form densely branched tree architectures through which mitochondria must be distributed to supply the cell's energetic needs. Dendritic mitochondria circulate across the tree, undergoing fusion and fission to form clusters of varying sizes. We present a mathematical model for the distribution of such actively driven interacting particles in a branched geometry, showing that the density and localization of particles is highly sensitive to the fusion/fission balance and to the tree architecture. Our model demonstrates that “balanced” trees (wherein cross-sectional area is conserved across junctions and thicker branches support more bushy subtrees) enable symmetric yet distally enriched particle distributions and promote dispersion into smaller clusters. These results highlight the importance of tree morphology and radius-dependent fusion in governing the distribution of neuronal mitochondria. Published by the American Physical Society2024