Participation of local communities in conservation is essential for long-term sustainability of biosphere reserves. Yet, questions remain about conditions under which participation is successful. Positive perceptions about a protected area, which may be associated with economic benefits or improved social capital, can promote pro-conservation behaviour, yet relationships are unclear. To assess this, we investigated perception–behaviour relationships in El Vizcaíno Biosphere Reserve, Mexico – a socially and ecologically diverse desert region. Unsustainable and illegal resource use in the reserve has placed ecosystems under pressure. A survey of 367 people in seven rural communities and informal interviews with stakeholders suggested there was strong support for reserve designation among respondents. While conservation was recognized as a primary purpose for designation, respondents perceived the reserve was threatened by illegal and unsustainable activities. Concomitantly, respondents desired effective regulatory management and socio-economic development. Positive perceptions did not translate into pro-conservation behaviour. Respondents were largely unaware of, and had rarely participated in, conservation initiatives. Reasons appear to be related to the limited capacity of government agencies and resource management institutions. The latter require continual external support to develop stronger leadership, management skills and more equitable governance, required to bring local actors into conservation.