台灣原生種姬蝴蝶蘭的葉綠體基因體的完整序列為148,959 bp。其結構含有一對反向重複序列 ( IRs； 25,846 bp )，將整個基因體分成一個大單複本區( LSC；85,967 bp )及一個小單複本區( SSC；11,300 bp )。姬蝴蝶蘭的葉綠體基因體含有109種基因，包含75個蛋白質基因、4個RNA基因、30個tRNA基因以及21個可能的ORF(≧225 bp )。其中17個基因含有插入子，包含6個 tRNA 及 11個蛋白質編碼基因，而clpP、rps12 及 ycf3更含有2個插入子。將姬蝴蝶蘭、台灣白花蝴蝶蘭、及文心蘭的葉綠體基因體做比較分析，發現無論在基因組成、AT含量、ndh基因與ycf1的插入/缺失分佈及邊界變異上，台灣白花蝴蝶蘭與姬蝴蝶蘭極為相近，而蝴蝶蘭與文心蘭間則有較大差異。三種蘭科植物在ndh基因及ycf1基因都有程度不一的序列缺失及基因遺失現象，台灣白花蝴蝶蘭遺失了ndhA, F 和H基因; 姬蝴蝶蘭則遺失了ndhA、E、F 和H基因。而台灣白花蝴蝶蘭及姬蝴蝶蘭在ndhE、G及I有較嚴重的序列缺失；文心蘭則遺失ndhF及K基因且在ndhB、D、J及ycf1有較嚴重的序列缺失。三種蘭科在LSC/IR邊界變異不大；然而，在SSC/IR 邊界變異較大。此外，將兩種原生種蝴蝶蘭間的葉綠體基因組做多型性的比較分析，結果顯示在IR區域都有較低的單核苷酸多型性( SNP )及插入/缺失變異( InDel )。另外,兩種台灣原生種蝴蝶蘭基因間，與光合作用電子傳遞鏈功能相關的基因在演化上較具保留性；而與基因表現功能有關的基因，則歧異度較大。

The complete chloroplast genome of P. equestris is 148,959 bp. A pair of inverted repeat (IRs; 25,846 bp) divides the genome into a large single copy region (LSC; 85,967 bp) and a small single copy region (SSC; 11,300 bp). There are 109 genes present in the chloroplast genome of P. equestris including 75 protein coding genes, 4 RNA genes and 30 tRNA genes. In addition, 21 putative ORF were identified with a threshold of 225 bp. Seventeen genes contain introns, including 6 tRNA and 11 protein coding genes, and clpP, rps12 and ycf3 have two introns. Comparative chloroplast genomic study among three species of orchid (P. equestris; P. aphrodite and Oncidium spp.) reveal that gene and AT content, the InDel of ndh and ycf1 genes as well as the variation of IR junction are more conserved between two Taiwan moth orchid than that of between Taiwan moth orchid and Oncidium spp. Lost of ndhA, H and F genes, and lost of ndhA, H, E and F genes were found in P. aphrodite and P. equestris, respectively, but lost of ndhF and ndhK was observed in Oncidium spp. In terms of the InDel in ndh and ycf1 genes among three species of orchid, serious truncation of ndhE, G and I were observed in P. equestris and P. aphrodite, in contrast, serious deletion of ndhB, D, J and ycf1 were found in Oncidium spp. There is no significant variation in LSC/IR border region among three species of orchid, in contrast, significant variation were observed in SSC/IR border region. Comparative chloroplast genomes between two Taiwan moth orchids also reveal lower rate of single nucleotide polymorphism (SNP) and insertion/deletion (InDel) in IR regions. In addition, the genes coding for photosynthetic apparatus are evolutionarily conserved and genes coding for genetic system are evolutionarily more divergent.

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