Delineating conservation units is a fundamental step in recovery planning for endangered species. Yet, challenges remain in the application and validation of scientifically evaluated conservation units in management practice. The Canadian government makes use of Designatable Units (DUs) as the primary conservation unit under their Species‐at‐Risk Act. DUs must be ecologically discrete and have demonstrated evolutionary significance, which, in the case of woodland caribou (Rangifer tarandus caribou), has led to the definition of multiple DUs across Canada. Simultaneously, Environment and Climate Change Canada has released two recovery strategies affecting four DUs, wherein DUs are subdivided into smaller conservation units. However, the two recovery strategies adopt different definitions for the conservation unit. For the Boreal DU, the Local Population is considered the conservation unit for recovery management, whereas for Southern Mountain DU, the conservation unit for recovery is the subpopulation, which may or may not be comprised of several Local Populations. The scientific rationale for the difference between recovery strategies is unclear, not necessarily supported by genetic or demographic evidence, and highlights a policy challenge facing caribou conservation. We argue that the current emphasis on protecting subpopulations within a DU might be inconsistent and unviable for recovery planning. Instead, the recognition and emphasis on maintaining meta‐population dynamics within DUs is essential and currently underutilized in the long‐term recovery of woodland caribou in Canada.