We studied the spatial and temporal patterns of decomposition of roots of a desert sub-shrub, a herbaceous annual, and four species of perennial grasses at several locations on nitrogen fertilized and unfertilized transects on a Chihuahuan Desert watershed for 3.5 years. There were few significant differences between the decomposition rates of roots on the NH₄NO₃ fertilized and unfertilized transects. Decomposition of all roots followed a two-phase pattern: early rapid mass loss followed by a long period of low mass loss. Rates of decomposition were negatively correlated with the initial lignin content of the roots (r=0.90). Mass loss rates of the roots of the herbaceous annual, Baileya multiradiata, were significantly higher than those of the grasses and the shrub, probably as a result of subterranean termites feeding on B. multiradiata root material. The only location where mass loss rates were significantly different was the dry lake bed, where mass loss rates were lower than those recorded on the upper watershed. The spatial differences in mass loss rates in the dry lake were attributable to the high clay content of the soils, which reduced water availability, and to the absence of termites. Non-polar substances in decomposing roots decreased rapidly during the first year, then decreased at a low but fairly constant rate. Water-soluble compounds decreased rapidly (50–60% of initial concentration) during the first 3–6 months. Lignin concentrations of roots of perennial grasses were higher than those of herbaceous annual plants and woody shrubs. Lignin concentrations increased in all species during decomposition. The chemical changes in decomposing roots followed the patterns described for decomposing litter in mesic environments.