IUCN Red List assessments are important for conservation and management initiatives. However, status assessments are often challenging because of poor sampling between biogeographical regions. Researchers sometimes assess poorly known species, which can have unforeseen ramifications, including the trade of rare and cryptic species under common species names. Here, we address this issue in relation to economically important reptile species in Indonesia. We reviewed examples of single species categorized as Least Concern for which the assessments probably encompassed multiple closely related species. We also examined Red List assessments that utilized species distribution modelling techniques, and identified biogeography as a major barrier to using such methods. To test how biogeography may affect status assessments we used our own model lizard system from Indonesia, taking an integrative phylogeographical approach to quantify status assessments under contrasting scenarios. We show that failure to account for biogeographical breaks leads to significant variation in Red List status. Our model system fluctuates from Least Concern to Endangered, depending upon whether biogeographical boundaries are considered in taxonomic evaluations. We identify Sauria (lizards) and Serpentes (snakes) as major lineages requiring taxonomic and conservation attention in Indonesia. We also make the following recommendations: (1) Indonesia's trade quotas should further subdivide management zones to account for gaps in taxonomic evaluations; (2) genetic sampling should be considered a high priority during wildlife exportation processes from poorly studied geographical areas; and (3) continuation of thorough biological inventory is critical for conservation initiatives across heterogeneous mountain and island landscapes.