Atacama is the most hyper-arid Desert in the world. In this study, we describe a novel species, Nakazawaea atacamensis f. a., sp. nov., isolated from plant samples in the Atacama Desert of Chile. In total, three isolates of N. atacamensis were obtained from independent Neltuma chilensis bark samples (synonym Prosopis chilensis, Algarrobo). The novel species was delineated based on morphological, physiological, biochemical, and molecular characteristics. A neighbour-joining analysis using the sequences of the D1/D2 domains of LSU rRNA revealed that N. atacamensis sp. nov. clustered with Nakazawaea pomicola. The sequence of N. atacamensis differed from closely related species by 1.3% to 5.2% in the D1/D2 domains. A phylogenomic analysis based on single nucleotide polymorphism’s data confirms that the novel species belongs to the genus Nakazawaea, and placed N. atacamensis closer to N. peltata. Phenotypic comparisons demonstrated that N. atacamensis sp. nov. exhibited distinct carbon assimilation patterns compared to its related species. Genome sequencing of the ATA-11A-B ^T strain revealed a genome size of approximately 12.4 Mbp, similar to other Nakazawaea species, with 5,116 protein-coding genes annotated using InterProScan. In addition, N. atacamensis exhibited the capacity to ferment synthetic wine must, representing a potential new yeast for mono or co-culture wine fermentations. This comprehensive study expands our understanding of the genus Nakazawaea and highlights the ecological and industrial potential of these yeasts in fermentation processes. The holotype of N. atacamensis sp. nov. is CBS 18375 ^T. The Mycobank number is MB 849680.