Symbionts have a unique mode of life that has attracted the attention of ecologists and evolutionary biologists for centuries. As a result of this attention, these disciplines have produced a mature body of literature on host-symbiont interactions. In contrast, the discipline of symbiont conservation is still in a foundational stage. Here, we aim to integrate methodologies for symbiont coevolutionary biology with symbiont conservation. We focus on host-symbiont cophylogenies, because they have been widely used to study symbiont diversification history and contain information on symbiont extinction. However, cophylogenetic information has never been used nor adapted to the perspective of conservation. Here, we propose a new statistic, “cophylogenetic extinction rate” (Ec), which is based on coevolutionary knowledge from event-based cophylogenetic analyses and could be informative to assess relative symbiont extinction risks. Finally, we propose potential future research to further develop methods to estimate symbiont extinction risk from cophylogenetic analyses, and to continue the integration of this existing knowledge of coevolutionary biology and cophylogenetics into future symbiont conservation studies and practices.