Many development projects intended to exploit natural resources are occurring in fragile ecosystems, and therefore the need for sound biodiversity assessment and monitoring programs is growing. Large mammals are important components of these fragile ecosystems, yet there are few strategies that attempt to assess and monitor entire large mammal communities in relation to development projects. We propose the use of two indices applied within a framework of adaptive management. An occurrence index assesses the composition and distribution of large mammals at a site, and an abundance index monitors the abundance of large mammals over time in relation to development. We discuss the design, applicability and effectiveness of these indices based on our experience with a natural gas development project in the Amazon forests of southeastern Peru.