Dr Ninan's research has focused on understanding the economics and institutional aspects of biodiversity conservation in the tropical forests of the Western Ghats biodiversity hotspot in Southern India which is one of the thirty-five biodiversity hotspots in the world. His work among the local communities of the tropical forests of the Western Ghats biodiversity hotspot is noteworthy. Besides economics and valuation of biodiversity and forest ecosystem services Dr. Ninan's research has focused on sustainable use and management of forest and water resources; sustainable agriculture; impact assessment of watershed and community forestry projects; climate resilience, adaptation and climate change impacts; and poverty studies.