The subtribe Orchidinae, distributed predominantly in Eastern Asia and the Mediterranean, presents some of the most intricate taxonomic problems in the family Orchidaceae with respect to generic delimitation. Based on three DNA markers (plastid matK, rbcL, and nuclear ITS), morphological characters, and a broad sampling of Orchidinae and selected Habenariinae mainly from Asia (a total of 153 accessions of 145 species in 31 genera), generic delimitation and phylogenetic relationships within the subtribe Orchidinae and Habenariinae from Asia were assessed. Orchidinae and Asian Habenariinae are monophyletic, and Orchidinae is divided into distinct superclades. Many genera, such as Amitostigma, Habenaria, Hemipilia, Herminium,Platanthera, Peristylus and Ponerorchis, are not monophyletic. Habenaria is subdivided into two distantly related groups, while Platanthera is subdivided into three even more disparate groups. Many previously undetected phylogenetic relationships, such as clades formed by the Amitostigma–Neottianthe–Ponerorchiscomplex, Platanthera latilabris group, Ponerorchis chrysea, Sirindhornia, and Tsaiorchis, are well supported by both molecular and morphological evidence. We propose to combine Hemipiliopsis with Hemipilia,Amitostigma and Neottianthe with Ponerorchis, Smithorchis with Platanthera, and Aceratorchis andNeolindleya with Galearis, and to establish a new genus to accommodate Ponerorchis chrysea. Tsaiorchisand Sirindhornia are two distinctive genera supported by both molecular data and morphological characters. A new genus, Hsenhsua, and 41 new combinations are proposed based on these findings.