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Gypsum soils (calcium sulfate) occur throughout arid regions of the world. These soils contain a large number of endemic plants. Limited information is available about the microbial symbionts of these plants. We collected eight endemic gypsophilous flowering plant species in New Mexico and characterized their root-and leaf-associated fungi using molecular, microscopic, and culture techniques. Dominant culturable fungi were identified by analysis of the internal transcribed spacer (ITS) rDNA region. Microscopic analysis of roots indicated that gypsophilous plants are colonized primarily by arbuscular mycorrhizal and dark septate fungi. Sporobolus nealleyi Vasey (a gypsophilous grass) showed the greatest percentages of fungal colonization. All fungal isolates belonged to the Ascomycota, dominated by the orders Pleosporales and Sordariales. Isolates in the Alternaria complex were the dominant fungi recovered from leaves, and Monosporascus was the dominant genus recovered from roots. The dominant genera show low plant specificity and wide distribution as plant symbionts in arid regions. The generalist nature of gypsophilous plants with respect to their fungal symbionts could be advantageous for their successful establishment and survival. A common cohort of fungal symbionts could facilitate efficient transfer of nutrients and water in these plants that are restricted to a specific substrate in an environment dominated by extreme conditions.