Abstract: Orchidaceae is a widespread plant family and Sri Lankan orchid flora represents 188 species belonging to 78 genera, including 01 endemic genus (Adrorhizon) and 55 endemic species. The main aim of the present research was to characterize selected species of genera Dendrobium and Bulbophyllum in Sri Lanka with respect to their ITS sequence data and to derive phylogenetic relationships. Modified CTAB protocol was followed for DNA extractions and ITS region was amplified using the primer sets of 17SE and 26SE and phylogenetic trees were constructed based on the available ITS sequences of the Asian species of Dendrobium and Bulbophyllum by MEGA7 software package. Genetic variation and relationships of six Sri Lankan orchid species; Dendrobium aphyllum, D. crumenatum, D. nutantiflorum endemic species of Bulbophyllum elliae, B. trimenii and Eria bicolor were determined using ITS sequencing. Findings of the analysis conclude, suitability of ITS sequencing as a molecular marker for deriving phylogenetic relationships of genera Dendrobium and Bulbophyllum with Eria as the out group. Further, indiscretions in derived relationships of these taxa with respect to ITS sequences can be interpreted as the effect of geographical isolation occurred during the continental drift.