BackgroundThe orchid genusPholidotaLindl. ex Hook. is economically important as some species has long been used in traditional medicine. However, the systematic status of the genus and intergeneric relationships inferred from previous molecular studies are unclear due to insufficient sampling and lack of informative sites. So far, only limited genomic information has been available. The taxonomy ofPholidotaremains unresolved and somewhat controversial. In this study, the complete chloroplast (cp.) genomes of thirteenPholidotaspecies were sequenced and analyzed to gain insight into the phylogeny ofPholidotaand mutation patterns in their cp. genomes.ResultsAll examined thirteenPholidotacp. genomes exhibited typical quadripartite circular structures, with the size ranging from 158,786 to 159,781 bp. The annotation contained a total of 135 genes in each cp. genome, i.e., 89 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The codon usage analysis indicated the preference of A/U-ending codons. Repeat sequence analysis identified 444 tandem repeats, 322 palindromic repeats and 189 dispersed repeats. A total of 525 SSRs, 13,834 SNPs and 8,630 InDels were detected. Six mutational hotspots were identified as potential molecular markers. These molecular markers and highly variable regions are expected to facilitate future genetic and genomic studies. Our phylogenetic analyses confirmed the polyphyletic status of the genusPholidota, with species grouped into four main clades:Pholidotas.s. was resolved as the sister to a clade containing species ofCoelogyne; the other two clades clustered together with species ofBulleyiaandPanisea, respectively; speciesP. ventricosawas placed at the basal position, deviated from all other species.ConclusionThis is the first study to comprehensively examine the genetic variations and systematically analyze the phylogeny and evolution ofPholidotabased on plastid genomic data. These findings contribute to a better understanding of plastid genome evolution ofPholidotaand provide new insights into the phylogeny ofPholidotaand its closely related genera within the subtribe Coelogyninae. Our research has laid the foundation for future studies on the evolutionary mechanisms and classification of this economically and medicinally important genus.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-023-04233-8.