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Summary Auxin is a critical phytohormone that is involved in the regulation of most plant growth and developmental responses. In particular, epigenetic mechanisms, like histone modifications and DNA methylation, were reported to affect auxin biosynthesis and transport. However, the involvement of other epigenetic factors, such as histone variant H2A.Z, in the auxin‐related developmental regulation remains unclear. We report that the histone variant H2A.Z knockdown mutant in Arabidopsis Col‐0 ecotype, h2a.z‐kd, has more lateral roots and weak gravitational responses related to auxin‐regulated growth performances. Further study revealed that auxin promotes the eviction of H2A.Z from the auxin‐responsive genes SMALL AUXIN‐UP RNAs (SAURs) to activate their transcriptions. We found that IAA promotes the transcription of H2A.Z genes through HOMEOBOX PROTEIN 22/25 (AtHB22/25) transcription factors which work as downstream targets of ARF7/19 in auxin signaling. Double mutant of hb22 hb25 showed similar lateral root and gravitropism phenotypes to h2a.z‐kd. Our results shed light on a reciprocal regulation hub through INOSITOL AUXOTROPHY 80‐mediated H2A.Z eviction and ARF7/19‐HB22/25‐mediated H2A.Z transcription to modulate the activation of SAURs and plant growth in Arabidopsis.