BackgroundThe taxonomy and infrageneric delimitation ofPhalaenopsisBlume has been significantly disputed due to some overlapping morphological features between species related, which needed further evidence for clarification. The structural characterization of complete chloroplast genomes ofP. storbatianaandP. wilsoniiwere analyzed and compared with those of related taxa to provide a better understanding of their genomic information on taxonomy and phylogeny.ResultsIt was shown that chloroplast genomes ofPhalaenopsis storbatianaandP. wilsoniihad a typical quadripartite structure with conserved genome arrangements and moderate divergence. The chloroplast genomes ofP. storbatianaandP. wilsoniiwere 145,885 bp and 145,445 bp in length, respectively, and shared a similar GC content of 36.8%. Gene annotations of two species revealed 109 single-copy genes consistently. In addition, 20 genes duplicated in the inverted regions, 16 genes each possessed one or more introns, and fivendh(NA (D)H dehydrogenase) genes were observed in both. Comparative analysis of the total cp genomes ofP. storbatianaandP. wilsoniiwith those of other six relatedPhalaenopsisspecies confirmed the stable sequence identity for coding and non-coding regions and higher sequence variation in SC regions than IR regions. Most of their protein-coding genes had a high degree of codon preference. Moreover, 45 genes were discovered with significantly positive selection. However, different amplifications in IR regions were observed in these eight species. Phylogenetic analysis based on CDS from 60 species representing main clades in Orchidaceae indicated thatPhalaenopsisspecies includingP. stobartianaandP. wilsoniiformed a monophyletic clade with high bootstrap nested in tribe Vandeae of Epidendroideae, which was consistent with those from previous studies.ConclusionsThe results could provide insight into understanding the plastome evolution and phylogenetic relationships ofPhalaenopsis.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-023-09448-5.