The Anthropocene is defined by unprecedented human influence on the biosphere. Integrative conservation recognizes this inextricable coupling of human and natural systems, and mobilizes multiple epistemologies to seek equitable, enduring solutions to complex socioecological issues. Although a central motivation of global conservation practice is to protect at-risk species, such organisms may be the subject of competing social perspectives that can impede robust interventions. Furthermore, imperiled species are often chronically understudied, which prevents the immediate application of data-driven quantitative modeling approaches in conservation decision making. Instead, real-world management goals are regularly prioritized on the basis of expert opinion. Here, I explore how an organismal natural history perspective, when grounded in a critique of established human judgements, can help resolve socioecological conflicts and contextualize perceived threats related to threatened species conservation and policy development. To achieve this, I leverage a multi-national system anchored by a diverse, enigmatic, and often endangered New World clade: alligator lizards. Using a threat analysis and status assessment, I show that one recent petition to list a California alligator lizard, Elgaria panamintina, under the US Endangered Species Act often contradicts the best available science. Building on this analysis, I also provide empirical evidence that the multi-species petition model under which Elgaria panamintina was proposed is problematic, thus corroborating claims made by the US Fish and Wildlife Service in their recent policy decision to ban such petitions. Shifting to Mesoamerica, I use global and regional status listings, distribution data, and a preliminary protected area gap analysis to show that an entire genus of alligator lizards (Abronia) is warranted for recognition as a flagship, despite conflicting social views toward the lizards. I supplement this finding with novel radio telemetry data on Abronia graminea, which reveals their strong arboreality, generalist forest habitat use, and adaptability to forest disturbance. Finally, I provide a checklist and bilingual dichotomous key for all 29 species of Abronia, and offer best-practice solutions to broader species identification problems in understudied regions of the world. My findings challenge conventional wisdom in this system, and showcase lessons of broad relevance to applied conservation that account for social and biological linkages.