Vanilloideae is one of the subfamily of Orchidaceae, and is composed of 14 genus and 245 species. In this study, six plastomes (Lecanorchis japonica, Lecanorchis kiusiana, Pogonia japonica, Pogonia minor, Vanilla planifolia and Vanilla madagascariensis) were newly sequenced. The Vanilloideae platomes ranged from 70,498 bp (Lecanorchis japonica) to 158,200 bp (Pogonia japonica). Two species of Lecanorchis have the mycoheterotrophic nutritional mode so that have bizarre plastomes which experience rRNA relocation, rearrangement and gene reduction. Other four species in Pogonia and Vanilla have the photosynthetic nutritional mode, which is expected to have typical Orchidaceae plastome. However, SSC contraction occurred in two Pogonia and two Vanilla plastomes. Nine inversions were observed among Apostasioideae and Vanilloideae. In the phylogenetic tree, Vanilloideae formed monophyly and located at traditional phylogenetic position. Synonymous and nonsynonymous substitution rates comparison was performed between Vanilloideae and Apostasioideae, which is most related subfamily of Vanlloideae. In dS likelihood ratio test, psaC, psbL and psbT were judged insignifcant (p-value > 0.05). Twelve regions (accD, atpF, cemA, rmatK, psaJ, psbN, bcL, rpl2, rpl20, rps4, rps18, ycf1) were found as significant that intensification or relaxation selective pressure worked.