Background and aims The Tehuacán-Cuitcatlán reserve is an area of unique plant biodiversity mostly in the form of xerophytes, with exceptionally high numbers of rare and endemic species. This endemism results partly from the characteristics of the climate of this area, with two distinct seasons: rainy and dry seasons. Although rhizosphere communities must be critical in the function of this ecosystem, understanding the structure of these communities is currently limited. This is the first molecular study of the microbial diversity present in the rhizosphere of Mamillaria carnea. Methods Total DNA was obtained from soil and rhizosphere samples at three locations in the Tehuacán Cuicatlán Reserve, during dry and rainy seasons. Temperature gradient gel electrophoresisis (TGGE) fingerprinting, 16S rRNA gene libraries and pyrosequencing were used to investigate bacterial diversity in the rhizosphere of Mammillaria carnea and changes in the microbial community between seasons. Results Deep sequencing data reveal a higher level of biodiversity in the dry season. Statistical analyses based on these data indicates that the composition of the bacterial community differed between both seasons affecting to members of the phyla Acidobacteria, Cyanobacteria, Gemmatimonadetes, Plantomycetes, Actinobacteria and Firmicutes. In addition, the depth of sequencing performed (>24,000 reads) enables detection of changes in the relative abundance of lower bacterial taxa (novel bacterial phylotypes) indicative of the increase of specific bacterial populations due to the season. Conclusions This study states the basis of the bacterial diversity in the rhizosphere of cacti in semi-arid environments and it is a sequence-based demonstration of community shifts in different seasons.