The creation of urban preserves has been proposed to as a method of reducing the impact of urbanization on biodiversity of native ecosystems. This research compared root colonization by two important fungal root symbionts, arbuscular mycorrhizal (AM) fungi and dark septate endophytes (DSE), at two urban desert preserve sites located in Phoenix, Arizona and at two surrounding Sonoran desert sites. Diversity of AM fungi was also compared between sites. AM root colonization was greater in surrounding deserts in comparison to urban preserves, but root colonization by DSE was not significantly different. A greater number of AM fungal species was detected in surrounding deserts in comparison to urban preserves, although the number of species/sample was not significantly different. About 70% of the AM fungal species were detected at both urban preserve and surrounding desert sites, but species in the family Acaulosporaceae were only detected at the surrounding deserts. Decreases in AM functioning and diversity observed at urban preserves may reduce the ability of preserves to sustain biodiversity.