The present provides molecular data for species of Habenaria diphylla (Nimmo) Dalzell, H. khasiana Hook.f. and H. rostellifera Rchb.f. collected from Binh Chau-Phuoc Buu Nature Reserve, Vietnam for the first time. Along with other DNA sequences from GenBank database, the phylogenetic trees for Habenaria species from Vietnam have been established.