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Conflict over endangered species conservation on military lands is becoming increasingly important as militaries attempt to balance an increased operational tempo with endangered species conservation. Successfully managing this conflict has major implications for biodiversity conservation given the US military alone manages over 12 million ha of land providing habitat to hundreds of at risk species, 24 of which are endemic to military installations. This paper provides the first assessment of this issue with a qualitative study of military trainers and civilian natural resource professionals who are employed by the Department of Defense (DoD) at the interface of endangered species conservation and troop training on installations throughout the Southeastern US. Emerging conflicts over endangered species conservation on DoD lands differed from non-military contexts because military structure forced interactions into strict protocols allowing avoidance, but not direct contention. Although all informants officially stated nothing impacted training, training area supervisors described endangered species conservation the greatest threat to training they faced. Despite pointed efforts to avoid engagement and official denial that conflict existed, interactions between the groups were characterized by deindividualization and communication breakdown, residues typically associated with highly escalated conflicts. These findings suggest suppressing conflict may create the same negative outcomes typically associated with prolonged direct conflict, by denying parties the ability to resolve differences. These negative outcomes can be addressed by both acknowledging biodiversity conservation conflict exists and allowing dissent during decision-making. Improved cooperation between TASU and NRECM can help reduce impacts of warfare on wildlife conservation, while ensuring sustainability of military training on lands critical to biodiversity conservation.