Most of the hundreds of citrus varieties are derived from spontaneous mutations. We characterized the dynamics of single‐nucleotide mosaicism in a 36‐yr‐old clementine (Citrus ×clementina hort. ex Tanaka) tree, a commercial citrus whose vegetative behavior is known in detail. Whole‐genome sequencing identified 73 reliable somatic mutations, 48% of which were transitions from G/C to A/T, suggesting ultraviolet (UV) exposure as mutagen. The mutations accumulated in sectorized areas of the tree in a nested hierarchy determined by the branching pattern, although some variants detected in the basal parts were also found in the new growth and were fixed in some branches and leaves of much younger age. The estimate of mutation rates in our tree was 4.4 × 10−10 bp−1 yr−1, a rate in the range reported in other perennials. Assuming a perfect configuration and taking advantage of previous counts on the number of total leaves of typical clementine trees, these mutation determinations allowed to estimate for the first time the total number of variants present in a standard adult tree (1,500–5,000) and the somatic mutations generated in a typical leaf flush (0.92–1.19). From an evolutionary standpoint, the sectoral distribution of somatic mutations and the habit of periodic foliar renewal of long‐lived plants appear to increase genetic heterogeneity and, therefore, the adaptive role of somatic mutations reducing the mutational load and providing fitness benefits.