BackgroundThe plant hormone auxin is widely involved in plant growth, development, and morphogenesis, and the TIR1/AFB and AUX/IAA proteins are closely linked to rapid auxin response and signal transmission. However, their evolutionary history, historical patterns of expansion and contraction, and changes in interaction relationships are still unknown.ResultsHere, we analyzed the gene duplications, interactions, and expression patterns ofTIR1/AFBsandAUX/IAAsto understand their underlying mechanisms of evolution. The ratios ofTIR1/AFBstoAUX/IAAsrange from 4:2 inPhyscomitrium patensto 6:29 inArabidopsis thalianaand 3:16 inFragaria vesca. Whole-genome duplication (WGD) and tandem duplication have contributed to the expansion of theAUX/IAAgene family, but numerousTIR1/AFBgene duplicates were lost after WGD. We further analyzed the expression profiles ofTIR1/AFBsandAUX/IAAsin different tissue parts ofPhyscomitrium patens,Selaginella moellendorffii,Arabidopsis thalianaandFragaria vesca, and found thatTIR1/AFBsandAUX/IAAswere highly expressed in all tissues inP. patens,S. moellendorffii. InA. thalianaandF. vesca,TIR1/AFBsmaintained the same expression pattern as the ancient plants with high expression in all tissue parts, whileAUX/IAAsappeared tissue-specific expression. InF. vesca, 11 AUX/IAAs interacted with TIR1/AFBs with different interaction strengths, and the functional specificity of AUX/IAAs was related to their ability to bind TIR1/AFBs, thus promoting the development of specific higher plant organs. Verification of the interactions among TIR1/AFBs and AUX/IAAs inMarchantia polymorphaandF. vescaalso showed that the regulation of AUX/IAA members by TIR1/AFBs became more refined over the course of plant evolution.ConclusionsOur results indicate that specific interactions and specific gene expression patterns both contributed to the functional diversification ofTIR1/AFBsandAUX/IAAs.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-023-04253-4.