Gynostemium is a putative floral structure formed by the fusion of the male and female reproductive parts (stamens and carpels) through a process during its development called synorganization. Most of the Indian species of Thottea Rottb. have a prominent gynostemium in their floral architecture, with varying degrees of adnation and complexity. Even though the gynostemium is a significant taxonomic marker for the inter-specific systematics in Thottea, the scepticism and arguments on deciphering its morphology and functional parameters, including the existence of staminodes, makes it imperative to be examined in detail. The present study is the first attempt in this line which aims to explore the morphological characters of gynostemium and reproductive biology of Thottea duchartrei Sivar., A.Babu and Balach., an endemic species in the Western Ghats. Stereo zoom microscopy, SEM and reproductive biological studies were conducted providing special emphasis to the gynostemium. Detailed analysis revealed the structural and functional diversity of gynostemium with regard to its components. The study also helped to recognize the columnar outgrowths on the gynostemium as staminodes. In total, the present study helps to solve the confusions regarding the functional identity of the gynostemium T. duchartrei with regard to its morphology.