Gastrochilus and related taxa is a diverse group of horticultural and threatened orchids occurring mainly in South-East Asia. Although Gastrochilus is a small genus, the generic and interspecific relationships of it are still not well understood. Here, we present a molecular study using sequence data from nuclear internal transcribed spacer (ITS) and four plastid DNA regions (matK, psbA-trnH, psbM-trnD, trnL-F) to clarify these relationships. Our results indicated that Gastrochilus is monophyletic and subdivided into five clades. Haraella is nested in Pomatocalpa, and together they are sister to Gastrochilus. Five morphological characters (epichile hairs, stem type, leaf size, dorsal sepal size and presence of leaf spots) agree well with the molecular phylogenetic trees and can be used to subdivide Gastrochilus. Two new species are separated from G. calceolaris, and the status of the confused species G. somai and G. fuscopunctatus is clarified as a distinct species. The molecular phylogenetic trees and evaluation of characters indicate that shifts in pollination system in Gastrochilus have occurred independently at least three times.