A considerable portion of the world's fungi is classified as microfungi; however, their inclusion in conservation plans has been limited because the vast majority of these organisms are identified through DNA sequencing technology and therefore cannot be easily enumerated or assigned discrete range boundaries. The IUCN Red List Categories and Criteria were primarily developed for extinction risk assessments of organisms whose distribution, abundance, and trends can be directly observed, making them difficult to apply to microscopic organisms. To address this challenge, we have developed a Microfungal Conservation Framework, which retains the logical structure of IUCN assessment criteria but replaces traditional metrics with those quantifiable using molecular occurrence data, detectability-adjusted occupancy, ecological specialization, functional importance, and degree of threat exposure. This framework is presented alongside worked examples demonstrating how sequence occurrences, habitat/host metadata, and threat layers can be combined to produce a transparent Microfungal Priority Index, even when taxonomy is incomplete or sampling coverage is limited. Ultimately, the MCF serves as a bridge between molecular ecology and conservation decision-making, facilitating the integration of microfungi into red-list assessments and spatial planning to address a significant gap in global biodiversity targets.