Background: Spatial patterns related to richness and endemism of Mexican ferns and lycophytes are not well known, particularly in highly biodiverse areas; among these, Oaxaca is considered a highly biodiverse Mexican state. Questions: Where are located the centers of richness and endemism of lycophytes and ferns in Oaxaca? Both groups of plants support the idea of beta-diverse state condition for Oaxaca? Study site and research period: The study includes all territory of Oaxaca, between 2015 and 2019. Methods: We analyzed the species distribution using grid cells of 20’ × 20’ of latitude and longitude as study units. For this, we applied species richness, endemism indexes (weighted endemism and corrected weighted endemism), and components of biodiversity (a, b and g), associated with a complementarity index. The distributional data of the species were mainly obtained from herbarium specimens. Results: The richness areas are concentrated in the Sierra Norte and Istmo regions. Three important areas in richness and endemic species are suggested from the endemism indexes. Most of the grid-cell combinations resulted in high values from the complementarity analysis suggesting a high species turnover. Conclusions: The diversity analyses suggested that Oaxaca is a beta-diverse state. The NOM-059 needs a serious, urgent, and critical revision for ferns and different biological groups. The Areas Voluntarily Designated for Conservation in Oaxaca play a major role in relation to Natural Protected Areas for conservation of ferns and lycophytes.