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We investigated seasonal dynamics of mycorrhizal colonization in response to precipitation in a Mojave Desert Larrea tridentata-Ambrosia dumosa shrub community as part of the overall Nevada Desert FACE (Free-Air CO2 Enrichment) Facility (NDFF) with the goal to understand carbon flow through desert ecosystems in the context of increased carbon availability associated with climate change. Arbuscular mycorrhizal (AM) fungal colonization of fine roots varied with season and with species in the co-dominant shrubs L. tridentata and A. dumosa at a site adjacent to the NDFF. We collected fine roots (< 1.0 mm diameter) at monthly intervals throughout 2001 and from October 2002 to September 2003 to quantify percent colonization via the line intercept method in cleared roots stained with trypan blue to visualize fungi. Colonization was highest in fall, increased throughout spring, and decreased during summer drought periods. Increases in colonization during summer and fall reflected increases in precipitation. Although peak precipitation occurred in spring, mycorrhizal colonization was not correspondingly high, suggesting that fine root initiation and growth, early season shoot growth, and flowering may have reduced carbon availability to the fungus.