Community Conservation has quite the history of working effectively with local people living near endangered species and rare habitats - often, they help them set up community-managed protected areas, sanctuaries, sustainable ecotourism...you name it. It depends on the community, because each village, culture, species they want to protect, and local ecosystem is unique. And they protect biodiversity by truly EMPOWERING people.
They work at the grassroots level, which means they're nimble and able to respond to what communities need quickly and efficiently. Based in Gays Mills, WI but with projects in many countries: Belize, Myanmar, Nepal, Ecuador, etc.
Full disclosure - I work here! I've only been here for about six months, but it has been an absolute pleasure learning about all the things my colleagues here (not to mention the organization's founder, Rob Horwich) have accomplished over the years.