Sanjay Gubbi won the award for his work to protect Karnataka's tiger corridors, and Purnima Barman for creating an all-female network to save the Greater Adjutant stork, known in India as Hargila, and its wetland habitat in Assam.
The two Indians are among six global winners of the award shortlisted from 166 entries.
Each of the winners receives 35,000 pounds (USD 45,374) prize money in project funding over one year.
"This is a life-changing event for my team. It is a dream of every conservationist to win this award and the prize money will go a long way in expanding our Hargila Army network," said Barman, who got attracted to the project while she worked on her PhD in Kamrup district of Assam.
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Through her NGO Aaranyak, Barman has mobilised her all- female local network towards sustainable livelihoods through weaving traditional Assamese scarves and saris that are then sold to raise funds for the conservation project.
"With this award money, we plan to scale up this work, encouraging households in the region to take pride in the species and protect the birds and their nesting trees," she said.
Gubbi had quit his job as an electrical engineer to work with nature and wildlife.
"Karnataka is home to the highest number of Bengal tigers in India and in 2015 the figure stood between 10 and 15. Our hope is to take it up to 100 over the next few years but this can only be done through working with the community," he said.
With his award money, Gubbi hopes to reduce deforestation in two important wildlife sanctuaries which connect several protected areas and act as corridors for tigers, allowing them to move between territories.
"The awards are about recognising progress, winning those small battles which cumulatively equate to change at the national level. In addition to the financial benefit of winning the award, winners receive professional communications training to turn scientists into ambassadors," said Edward Whitley, founder of the Whitley Fund for Nature, which set up the awards 24 years ago.
The other winners of this year's awards include Indira Lacerna-Widmann from the Philippines for her project of partnering with prisoners to safeguard the critically endangered Philippine cockatoo.
The Whitley Fund for Nature is a UK-based charity that works to highlight grassroots leaders in nature conservation across the developing world.
This year's winners will be felicitated at a special ceremony at the Royal Geographic Society in London tomorrow and receive their awards from Queen Elizabeth II's daughter Princess Anne, The Princess Royal, who is a patron of the charity.