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Diversity and geographic distribution of cacti in the Cuatro Cienegas Basin (CCB), in the state of Coahuila, Northeast Mexico, were assessed using the complementary index (CI) and the geographic expansion index (GEI) in order to define priority zones for conservation from January 2017 to December 2018. The study area was divided into 12 plots, each of an area of approximately 192.93 km2. For each site, two rectangular plots were defined, each 1 km long and 40 m wide (i.e., a total 8 hectares of sample area per site), where cactus diversity, vegetation and soil types, and climate were recorded. Results showed the presence of 21 genera and 65 taxa including 42% and 12% of the taxa mentioned in the literature for the state of Coahuila, highlighting the richness of this area in the state. Cylindropuntia leptocaulis had the widest geographic distribution in CCB with GEI = 1.00, followed by eight taxa, whereas Echinomastus mariposensis, Echinomastus warnockii, and Epithelantha micromeris subsp. bokei had a narrower distribution with GEI = 0.1667 in CCB. Plot 3 (El Churince 1) was considered as a first priority site with a CI = 85% (55 taxa), followed by plot 2 (La Jara) with 8 taxa (CI = 8), and by site 7 San Juan with two additional taxa (CI = 3). Regarding priority sites for conservation, plot 2 (La Jara) had the highest number of threatened taxa (19) and a CI = 76%; this was followed by plot 3 (Churince 1) with 5 taxa endangered, (CI = 20%) and plot 7 was the last with only 1 taxa (CI = 4%). These plots are located in two vegetation types, the rosetophyllic desertic thornscrub and the microphyllic desertic thornscrub, with a semi-arid desertic climate (BWhw); soils include regosol, calcisol, and leptosol. Due to these environmental characteristics, CCB should be considered a hotspot zone regarding cacti species diversity in northeastern Mexico, and it is important to establish biodiversity conservation actions in the plots in CCB with the highest concentration of cacti species.