Short- and long-distance circadian communication is essential for integration of temporal information. However, a major challenge in plant biology is to decipher how individual clocks are interconnected to sustain rhythms in the whole plant. Here we show that the shoot apex is composed of an ensemble of coupled clocks that influence rhythms in roots. Live-imaging of single cells, desynchronization of dispersed protoplasts, and mathematical analysis using barycentric coordinates for high-dimensional space show a gradation in the strength of circadian communication in different tissues, with shoot apex clocks displaying the highest coupling. The increased synchrony confers robustness of morning and evening oscillations and particular capabilities for phase readjustments. Rhythms in roots are altered by shoot apex ablation and micrografting, suggesting that signals from the shoot apex are able to synchronize distal organs. Similarly to the mammalian suprachiasmatic nucleus, shoot apexes play a dominant role within the plant hierarchical circadian structure. Display omitted •Shoot apex clocks function as the suprachiasmatic nucleus neurons in mammals•Circadian coupling defines the high degree of synchrony among shoot apex clocks•The shoot apex clocks influence the circadian activity in roots•Different plant organs exhibit variations in clock precision and circadian synchrony The plant shoot apex clocks resemble the suprachiasmatic nucleus in mammals in their coupling properties and their capacity to synchronize circadian rhythms in distal organs.