Bulbophyllum odoratissimum (Sm.) Lindl. ex Wall. is widely used as traditional medicine for the treatment of tuberculosis, chronic inflammation and is listed as an endangered orchid due to over-exploitation and habitat destruction. The present study was carried out to establish a genetically stable in vitro regeneration protocol for mass multiplication using nodal segments and to determine phytochemical constituents, the antioxidant capacity of different parts (leaf, pseudobulb and root) of mother plants and acclimatized in vitro raised plants of B. odoratissimum. The synergistic effect of BA (4.0 mgl−1) and IBA (0.5 mgl−1) was found to be optimum for producing maximum shoot proliferation. IBA was found to be more effective for root proliferation than IAA, NAA and an average (3.08 roots/shoot) was obtained in 0.5 mgl−1 IBA. The well rooted plantlets were successfully acclimatized (more than 90% survival rate) in greenhouse, exhibiting normal development. The ISSR banding profiles confirmed high degree of genetic homogeneity among the clones. Extraction of all plant material from both mother plant and in vitro raised plant possess relevant TPC, TFC, radical scavenging activity (DPPH and ABTS) as well as total reducing power ability. HPLC chromatogram exhibited that phytochemical compounds detected in regenerated plants were similar to those present in mother plant and there was no remarkable difference. High regeneration frequency along with its genetic stability and secondary metabolite production validate the efficiency of this micropropagation protocol of B. odoratissimum for species recovery program as well as a potential source of commercial application.