We evaluated arbuscular mycorrhizal (AM) species diversity and abundance in nine locations along an anthropogenic nitrogen deposition gradient in coastal sage scrub (CSS) vegetation in southern California. The primary pollutants were nitrogen oxides derived from vehicular emissions. Extractable soil N on the gradient ranged from 5 to 87 μg/g during the summer months. For comparative purposes, we also assessed AM communities in nitrogen-fertilized (60 kg N·ha−1·yr−1) and unfertilized plots. Nitrogen enrichment induced a shift in AM community composition. In particular, an increasing input of nitrogen was associated with the displacement of the larger-spored species of Scutellospora and Gigaspora (due to a failure to sporulate) with a concomitant proliferation of small-spored Glomus species (e.g., Glomus aggregatum, Glomus leptotichum). A subsequent reduction in species richness and diversity (as measured by Shannon–Wiener index) accompanied eutrophication. Nitrogen enrichment also significantly reduced spore abundance, modified the timing of AM spore production in the most eutrophied site, and reduced hyphal and vesicular root infection. The fertilization experiment yielded similar patterns to those found along the gradient, and hence nitrogen input most likely explains the relationship between anthropogenic pollution and shifts in the AM communities. Such changes also indicated that AM species were sensitive indicators of nitrogen enrichment. The CSS is currently undergoing a conversion to Mediterranean annual grasslands, especially in the more urban polluted areas, and the shifts in the mycorrhizal fungal community may facilitate grass dominance in this system.