Background <p>The rhizosphere microbiota is vital for the modulation of plant growth and adaptation, especially in extreme environments. <i>Nitrophila atacamensis</i> is an endemic and endangered plant species in the Salar de Atacama, Chile. However, the specific relationships between <i>N. atacamensis</i> and its microbiota remain largely unknown. We analyzed the bacterial communities in the rhizosphere and bulk soils associated with <i>N. atacamensis</i> across eight sites, including Aguas de Quelana and Soncor, which are two distinct hydrogeological systems.</p> Results <p>We used high-throughput sequencing of the 16S rRNA gene to classify 886 different bacterial genera from 13,138 unique operational taxonomic units, distributed between rhizosphere and bulk soil samples. Microbial composition and diversity differed significantly between the rhizosphere and bulk soils. The microbial clustering observed among the Aguas de Quelana sites was based on their bacterial profiles and not their physicochemical properties, whereas the Soncor system exhibited high microbial heterogeneity. These findings suggest a potential role for water dynamics in shaping bacterial communities in Aguas de Quelana. Furthermore, the rhizosphere samples clustered into three distinct clades based on microbial composition; Pir4 lineage, <i>Aliifodinibius</i>, and <i>Candidatus</i> Tremblaya genera dominated specific clades.</p> Conclusions <p>This study provides the first comprehensive characterization of the rhizosphere and bulk soil bacterial diversity associated with <i>N. atacamensis</i>, providing important ecological and functional insights into its microbial interactions. This further highlights the importance of understanding the rhizosphere microbial diversity in extreme environments and its potential implications for biotechnological applications and conservation efforts. Our findings provide a foundation for future research on microbial–plant interactions in arid ecosystems.</p>