Cloud forests are ecosystems with a restricted distribution and high biodiversity, but they are highly threatened due to land use change. The objective of this study is to evaluate and prioritize existing cloud forest fragments to achieve their long-term conservation, combining threat levels and the potential response capacity of various conservation instruments in Mexico, through a triage tool. Threat levels were calculated based on human disturbance coverage, estimated specifically for Mexico. The response capacity was estimated using the presence of the different conservation instruments in each fragment. Once the triage level per fragment was obtained, these were analyzed by ecoregion. The results showed that the area of primary cloud forest, has been reduced between 53–73%, and only 31.6% (including primary and secondary forest) is under some protection scheme. We identified a group of fragments on the Pacific slope that require special attention due to the small coverage and their high level of priority. The ecoregions: Sierra Madre del Sur of Guerrero and Oaxaca, Los Altos de Chiapas, Sierra Madre Oriental and Central Mexico corresponding to the largest concentration of cloud forest in the trans-Mexican volcanic belt,70% of which are listed as a priority for emergency protection.