Bolivia’s National Programme of Conservation and Sustainable Utilization (PNCASL) for the customary harvest and conservation of caiman (Caiman yacare) illustrates a case study of the successful integration of indigenous and local knowledge (ILK) into biodiversity models to inform policy options (Llobet et al., 2004; Van Damme et al., 2007; Campos et al., 2010). Following the increasing engagement of local communities in PNCASL, new biological, socio-economic and cultural indicators of species health and abundance were developed and trialled. These included both biological indicators (based on models of the species) and socio-economic and cultural indicators of species health. One of the first trials took place in the Indigenous Territory and National Park Isiboro Sécure (TIPNIS), where local knowledge was initially the most reliable source on the status of Caiman yacare. Here, traditional knowledge on the status of caiman was incorporated into the development of robust indicators to inform resource quotas for customary harvest within this protected area. Traditional resource users participated in workshops where they defined concepts, harmonised criteria and conceptualised traditional knowledge of caiman habitats and territories into spatial maps. Population abundance was measured by scientific researchers, comparing estimates using both scientific techniques and indigenous techniques suggested by the communities (Aguilera et al., 2008). Models for estimating population abundance were adapted to make use of indigenous techniques of estimating caiman abundance and to incorporate qualitative indicators such as individuals’ perceptions of changes in caiman abundance, for example accounting for information from statements such as ‘there are a lot more caiman than before’. The process was repeated with communities across the TIPNIS territorial region, using this integration of knowledge systems and harvest estimates developed from local knowledge, and fortified with scientific concepts and criteria (e.g. sizes of hunt allowed) that were internalised by the local communities. This integrated process yielded a combined caiman population estimate for the protected area based on local knowledge.