BackgroundTheSinodielsiaclade of the subfamily Apioideae (Apiacieae) was established in 2008, and it is composed of 37 species from 17 genera. Its circumscription is still poorly delimited and unstable, and interspecific relationships in the clade lack comprehensive analysis. Chloroplast (cp.) genomes provide valuable and informative data sources for evolutionary biology and have been widely used in studies on plant phylogeny. To infer the phylogenetic history of theSinodielsiaclade, we assembled complete cp. genomes of 39 species and then performed phylogenetic analysis based on these cp. genome sequence data combined with 66 published cp. genomes from 16 genera relative to the Sinodielsia clade.ResultsThese 39 newly assembled genomes had a typical quadripartite structure with two inverted repeat regions (IRs: 17,599–31,486 bp) separated by a large single-copy region (LSC: 82,048–94,046 bp) and a small single-copy region (SSC: 16,343–17,917 bp). The phylogenetic analysis showed that 19 species were clustered into theSinodielsiaclade, and they were divided into two subclades. Six mutation hotspot regions were detected from the whole cp. genomes among theSinodielsiaclade, namely,rbcL–accD,ycf4–cemA,petA–psbJ,ycf1–ndhF,ndhF–rpl32 andycf1, and it was found thatndhF–rpl32 andycf1 were highly variable in the 105 sampled cp. genomes.ConclusionTheSinodielsiaclade was subdivided into two subclades relevant to geographical distributions, except for cultivated and introduced species. Six mutation hotspot regions, especiallyndhF–rpl32 andycf1, could be used as potential DNA markers in the identification and phylogenetic analyses of theSinodielsiaclade and Apioideae. Our study provided new insights into the phylogeny of theSinodielsiaclade and valuable information on cp. genome evolution in Apioideae.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-023-04271-2.