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Quantifying the controls on soil respiration is important for understanding ecosystem physiology and for predicting the response of soil carbon reservoirs to climate change. The majority of soil respiration is typically considered to occur in the top 20-30 cm of soils. In desert soils, where organic matter concentrations tend to be low and plants are deeply rooted, deeper respiration might be expected. However, little is known about the depth distribution of respiration in dryland soils. Here we show that the average depth of soil respiration between pulse precipitation events is almost always greater than 20 cm and is frequently greater than 50 cm in two central New Mexico desert shrublands. The average depth of soil respiration in a pinon-juniper woodland was shallower, between 5 and 40 cm. In the shrublands, 8 parts per thousand seasonal variations in the carbon isotope composition of soil-respired CO2 (delta C-13(r-soil)) that correlate with vapor pressure deficit support root/rhizosphere respiration as the dominant source of soil CO2. Such deep autotrophic respiration indicates that shrubs preferentially allocate photosynthate to deep roots when conditions near the surface are unfavorable. Therefore, respiration rates in these soils are not necessarily correlated with root biomass. The delta(13) Cr-soil values provide no evidence for CO2 evolved from soil inorganic carbon. Our results also suggest that organic carbon cycling is rapid and efficient in these soils and that the delta C-13 value of CO2 respired from soils in much of the southwestern US, and perhaps in other semiarid regions, varies seasonally by at least 4 parts per thousand.