BackgroundCeratostigma, a genus in the Plumbaginaceae, is an ecologically dominant group of shrubs, subshrub and herb mainly distributed in Qinghai-Tibet Plateau and North China.Ceratostigmahas been the focal group in several studies, owing to their importance in economic and ecological value and unique breeding styles. Despite this, the genome information is limited and interspecific relationships within the genusCerotastigmaremains unexplored. Here we sequenced, assembled and characterized the 14 plastomes of five species, and conducted phylogenetic analyses ofCerotastigmausing plastomes and nuclear ribosomal DNA (nrDNA) data.ResultsFourteenCerotastigmaplastomes possess typical quadripartite structures with lengths from 164,076 to 168,355 bp that consist of a large single copy, a small single copy and a pair of inverted repeats, and contain 127–128 genes, including 82–83 protein coding genes, 37 transfer RNAs and eight ribosomal RNAs. All plastomes are highly conservative and similar in gene order, simple sequence repeats (SSRs), long repeat repeats and codon usage patterns, but some structural variations in the border of single copy and inverted repeats. Mutation hotspots in coding (Pi values > 0.01:matK,ycf3,rps11,rps3,rpl22andndhF) and non-coding regions (Pi values > 0.02:trnH-psbA,rps16-trnQ,ndhF-rpl32andrpl32-trnL) were identified among plastid genomes that could be served as potential molecular markers for species delimitation and genetic variation studies inCerotastigma. Gene selective pressure analysis showed that most protein-coding genes have been under purifying selection except two genes. Phylogenetic analyses based on whole plastomes and nrDNA strongly support that the five species formed a monophyletic clade. Moreover, interspecific delimitation was well resolved exceptC.minus, individuals of which clustered into two main clades corresponding to their geographic distributions. The topology inferred from the nrDNA dataset was not congruent with the tree derived from the analyses of the plastid dataset.ConclusionThese findings represent the first important step in elucidating plastome evolution in this widespread distribution genusCerotastigmain the Qinghai-Tibet Plateau. The detailed information could provide a valuable resource for understanding the molecular dynamics and phylogenetic relationship in the family Plumbaginaceae. Lineage genetic divergence withinC.minuswas perhaps promoted by geographic barriers in the Himalaya and Hengduan Mountains region, but introgression or hybridization could not be completely excluded.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-023-04323-7.