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The coordination of light and hormone signaling is essential for the regulation of plant growth and development. Cytokinin signaling is mediated by a multistep phosphorelay (MSP) pathway, but its regulation by light remains incompletely understood. Here we investigate the role of phytochrome A (phyA) in the modulation of cytokinin signaling under far-red light conditions. Using a cytokinin-responsive reporter system, we observed a rapid suppression of MSP activity following far-red illumination, indicating that phyA acts as a negative regulator of cytokinin-mediated responses. Protein interaction analyses revealed that phyA physically interacts with the histidine phosphotransfer protein AHP3. Mass spectrometry identified a conserved serine motif (Ser87–90) in AHP3 as a phosphorylation site. Functional analyses suggest that serine phosphorylation of AHP3 affects its affinity for histidine kinase receiver domains and inhibits phosphate binding at the histidine residue, thereby modulating phosphotransfer efficiency in the MSP pathway. These findings indicate that phyA-mediated phosphorylation of AHP3 represents a regulatory mechanism linking far-red light perception with cytokinin signaling.