Blepharoglossumis a rare orchid genus of the Malaxidinae primarily distributed in tropical Pacific islands, with several species occurring in the Taiwan and Hainan Islands of China. Currently, the monophyletic status ofBlepharoglossumhas been challenged, and the phylogenetic relationships among its allied groups have remained unresolved with traditional DNA markers. In this study, we initially sequenced and annotated the chloroplast (cp) genomes of twoBlepharoglossumspecies,Blepharoglossum elegans(Lindl.) L. Li andBlepharoglossum grossum(Rchb.f.) L. Li. These cp genomes ofBlepharoglossumshare the typical quadripartite and circular structure. Each of the genomes encodes a total of 133 functional genes, including 87 protein-coding genes (CDS), 38 tRNA genes and 8 rRNA genes. By comparing the sequence differences between these two cp genomes, it was found that they are relatively conserved in terms of overall gene content and gene arrangement. However, a total of 684 SNPs and 2664 indels were still identified, withycf1,clpP, andtrnK-UUU protein-coding genes having the highest number of SNPs and indels. In further comparative analyses among the six cp genomes in Malaxidinae, significant sequence divergences were identified in the intergenic regions, namelyrps16–trnQ-UUG,trnS-GCU–trnG-GCC,rpoB–trnC-GCA,trnE-UUC–trnT-GGU,trnF-GAA–trnV-UAC,atpB–rbcL,petA–psbJ,psbE–petL,psbB–psbT,trnN-GUU–rpl32,trnV-GAC–rps7, andrps7–trnL-CAA, and five coding regions, includingmatK, andrpoC2,ycf1, and twoycf2 genes. Phylogenetic analysis indicated thatBlepharoglossumandOberoniaform a highly supported sister group relationship. Our results are consistent with previous studies and present increased resolution among major clades.