Biological soil crusts are an integral part of dryland ecosystems. We monitored the cover of lichens and mosses, cyanobacterial biomass, concentrations of UV-protective pigments in both free-living and lichenized cyanobacteria, and quantum yield in the soil lichen species Collema in an undisturbed Mojave Desert shrubland. During our sampling time, the site received historically high and low levels of precipitation, whereas temperatures were close to normal. Lichen cover, dominated by Collema tenax and C. coccophorum, and moss cover, dominated by Syntrichia caninervis, responded to both increases and decreases in precipitation. This finding for Collema spp. at a hot Mojave Desert site is in contrast to a similar study conducted at a cool desert site on the Colorado Plateau in SE Utah, USA, where Collema spp. cover dropped in response to elevated temperatures, but did not respond to changes in rainfall. The concentrations of UV-protective pigments in free-living cyanobacteria at the Mojave Desert site were also strongly and positively related to rainfall received between sampling times (R² values ranged from 0.78 to 0.99). However, pigment levels in the lichenized cyanobacteria showed little correlation with rainfall. Quantum yield in Collema spp. was closely correlated with rainfall. Climate models in this region predict a 3.5–4.0 °C rise in temperature and a 15–20% decline in winter precipitation by 2099. Based on our data, this rise in temperature is unlikely to have a strong effect on the dominant species of the soil crusts. However, the predicted drop in precipitation will likely lead to a decrease in soil lichen and moss cover, and high stress or mortality in soil cyanobacteria as levels of UV-protective pigments decline. In addition, surface-disturbing activities (e.g., recreation, military activities, fire) are rapidly increasing in the Mojave Desert, and these disturbances quickly remove soil lichens and mosses. These stresses combined are likely to lead to shifts in species composition and the local extirpation of some lichen or moss species. As these organisms are critical components of nutrient cycling, soil fertility, and soil stability, such changes are likely to reverberate throughout these ecosystems.