Fermented beverages made from cactus fruits hold deep historical, cultural, and nutritional significance in arid and semi-arid regions of Mexico and the United States. Despite their longstanding role in local diets and food systems, these beverages remain understudied in ethnobiological research. One example is colonche, a traditional beverage made by open fermentation of prickly pear fruits, particularly Opuntia streptacantha, in the Central Mexican Plateau. Similarly, the Comcaac (Seri) people of the Sonoran Desert prepare im & aacute;m hamaax (pitahaya wine) from Pachycereus pringlei fruit. This study combines ethnographic and microbiological approaches to investigate the production of these two beverages and their associated microbial communities. We documented traditional knowledge about harvesting, preparation, and fermentation practices in both regions. Forty-three yeast isolates were obtained from these fermented beverages, representing 12 species from 10 genera. These included both Saccharomyces and non-Saccharomyces yeast species, such as Kluyveromyces marxianus, Zygosaccharomyces bailii, Torulaspora delbrueckii, Meyerozyma guilliermondii, and Rhodotorula mucilaginosa. We observed regional differences in yeast composition, reflecting local ecological conditions and fermentation practices. This study contributes to the ethnobiology of traditional fermentations by documenting the microbial and cultural diversity of cactus-based beverages and highlighting the depth of the traditional ecological knowledge that sustains them. Our findings suggest that these fermentation systems provide valuable insights into microbial management, signs of domestication, biocultural resilience, and food heritage in arid environments.