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Recent droughts in southwestern USA have led to large-scale mortality of pinon (Pinus edulis) in pinon-juniper woodlands. Pinon mortality alters soil moisture, nutrient and carbon availability, which could affect the root-associated fungal (RAF) communities and therefore the fitness of the remaining plants. We collected fine root samples at a pinon-juniper woodland and a juniper savannah site in central New Mexico. Roots were collected from pinon and juniper (Juniperus monosperma) trees whose nearest neighbors were live pinon, live juniper or dead pinon. RAF communities were analyzed by 454 pyrosequencing of the universal fungal ITS region. The most common taxa were Hypocreales and Chaetothyriales. More than 10% of ITS sequences could not be assigned taxonomy at the phylum level. Two of the unclassified OTUs significantly differed between savanna and woodland, had few like sequences in GenBank and formed new fungal clades with other unclassified RAF from arid plants, highlighting how little study has been done on the RAF of arid ecosystems. Plant host or neighbor did not affect RAF community composition. However, there was a significant difference between RAF communities from woodland vs. savanna, indicating that abiotic factors such as temperature and aridity might be more important in structuring these RAF communities than biotic factors such as plant host or neighbor identity. Ectomycorrhizal fungi (EM) were present in juniper as well as pinon in the woodland site, in contrast with previous research, but did not occur in juniper savanna, suggesting a potential shared EM network with juniper RAF richness was lower in hosts that were neighbors of the opposite host. This may indicate competitive exclusion between fungi from different hosts Characterizing these communities and their responses to environment and plant neighborhood is a step toward understanding the effects of drought on a biome that spans 19 000 000 ha of southwestern USA.