Mexico has the fifth place among megadiverse countries, and the southern part of the country belongs to the Mesoamerican hotspot, where Oaxaca state has a very rich flora, related to its intricate topography. In this study, a multicriteria analysis (species richness, rareness, irreplaceability, turnover, and vulnerability) was used to prioritize conservation areas in Oaxaca, using as model system the genus Quercus (oaks), due to its high diversity and ecological importance. Our results indicate that the Sierra Madre de Oaxaca (SMOax) is the physiographic subprovince with the highest richness (38 species), rareness and irreplaceability of Quercus species, followed by the Montañas y Valles del Occidente (MVO; 29 species), the Sierra Madre del Sur (SMS; 25 species), and the Montañas y Valles del Centro (20 species). Areas that have retained most primary vegetation cover from 2000 to 2010 are mainly in the SMOax, in the Ixtlán district, and in the SMS, in the Miahuatlán district. On the other hand, MVO is the area with greater habitat disturbance, mainly in the Juxtlahuaca-Tlaxiaco districts. Oaxaca has numerous areas without official protection, named Indigenous Conservation and Community Areas, which play a central role as an alternative for conservation for 11 oak species. In conclusion, the priority conservation areas for the genus are mainly located in the SMOax and in the SMS. For white oaks, the semiarid area of Coixtlahuaca-Teposcolula-Nochitlán is important, while for the red oaks, the most important regions are the humid areas of Teotitlán, Sola de Vega, and Miahuatlán.