The Martin Ennals Foundation said that Alejandra Ancheita was picked ahead of posthumous nominee Cao Shunli -- a Chinese dissident who died in detention in March -- and Bangladeshi rights lawyer Adilur Rahman Khan.
"Alejandra Ancheita's selection by the jury highlights the array of forces facing human rights defenders," said Micheline Calmy-Rey, the former Swiss foreign minister who chairs the foundation.
Ancheita, who is the founder and executive director of the Mexican organisation ProDESC, has spent the past 15 years working to protect land and labour rights from transnational mining and energy companies.
The individuals and communities that she helps have sometimes faced violent attacks.
The Martin Ennals Award, named after the former secretary general of Amnesty International, is given to human rights defenders who show deep commitment to their cause despite huge personal risk.
"In Mexico, there is a clear pattern of attacks, threats, criminalisation, and murders of human rights defenders. Ms. Ancheita and ProDESC have been subjected to surveillance, a defamation campaign in the national media, and a break in at their offices," it said.
Ancheita was a pioneer in seeking justice in Mexican courts when companies failed to take local communities' rights into account, it added.
The award was created in 1993, two years after Ennals died.
Its jury is composed of Amnesty International, Human Rights Watch, the International Commission of Jurists and seven other international campaign organisations.
The laureate receives a prize of 20,000 Swiss francs (16,600 euros, $20,700).
The debut recipient in 1994 was Chinese rights activist and former political prisoner Harry Wu, who moved to the United States in the mid-1980s.
The award can also go to a group.
Last year's laureate was the Russia-based watchdog the Joint Mobile Group, honoured for its efforts to tackle abuses in Chechnya.
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