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Background   Paphiopedilum  is the largest genus of slipper orchids. Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat  ( IR) expansion and small single copy (SSC) contraction of the chloroplast genomes of  Paphiopedilum .    Results  Here, we sequenced, assembled, and annotated 77 plastomes of  Paphiopedilum  species (size range of 152,130 – 164,092 bp). The phylogeny based on the plastome resolved the relationships of the genus except for the phylogenetic position of two unstable species. We used phylogenetic and comparative genomic approaches to elucidate the plastome evolution of  Paphiopedilum . The plastomes of  Paphiopedilum  have a conserved genome structure and gene content except in the SSC region. The large single copy/inverted repeat (LSC/IR) boundaries are relatively stable, while the boundaries of the inverted repeat and small single copy region (IR/SSC) varied among species. Corresponding to the IR/SSC boundary shifts, the chloroplast genomes of the genus experienced IR expansion and SSC contraction. The IR region incorporated one to six genes of the SSC region. Unexpectedly, great variation in the size, gene order, and gene content of the SSC regions was found, especially in the subg.  Parvisepalum . Furthermore,  Paphiopedilum  provides evidence for the ongoing degradation of the  ndh  genes in the photoautotrophic plants. The estimated substitution rates of the protein coding genes show accelerated rates of evolution in  clpP ,  psbH , and  psbZ . Genes transferred to the IR region due to the boundary shift also have higher substitution rates.    Conclusions  We found IR expansion and SSC contraction in the chloroplast genomes of  Paphiopedilum  with dense sampling, and the genus shows variation in the size, gene order, and gene content of the SSC region. This genus provides an ideal system to investigate the dynamics of plastome evolution.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03053-y.

The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions