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While nostocacean cyanobacteria are ubiquitous and play critical roles in terrestrial ecosystems, their taxonomy and biogeography still entail mysteries. We isolated twoNostoc‐like cyanobacteria from biological soil crusts of the Atacama (Chile) and Mojave (USA) Deserts. An initial 16S rRNA gene phylogeny placed both in monophyly withMojavia pulchra. Here, we describe two new species of the previously monotypicMojaviausing a polyphasic approach including morphology, 16S rRNA phylogenies, secondary structure, and percent similarity of the 16S‐23S ITS region. LikeM. pulchra, both new species produce compact microcolonies, arthrospore‐like akinetes, and monocytes, traits characteristic of the genus.Mojavia aguileraesp. nov. is morphologically distinct from both other species in producing bluntly conical end cells, abundant enlarged akinetes in multiseriate filaments, and gold‐colored cells during senescence.Mojavia dolomitestrissp. nov. exhibited distinctly firm, light‐colored, compartmentalized mucilage.M. dolomitestrisis somewhat cryptic withM. pulchra, but has more densely packed microcolonies, rarity and later onset of brownish sheath pigmentation, and an origin from soils derived from dolomite. The two new species strengthened the position ofMojaviaas a robust genus sister toNostoc.Although 16S rRNA gene data could not separate theMojaviaspecies from each other, the three species showed distinct dissimilarities in secondary ITS structure and differed greatly fromNostocsensu stricto.The high dissimilarities between their 16S‐23S ITS regions suggest a long evolutionary history of the three species as separate lineages.Mojaviais an evolutionary and ecologically unique nostocacean genus, and its rarity and restricted habitat point to an urgent need for recognition and protection.