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We study the retrieval of surface and deep moisture of bare soil from noisy radar observations using simulated annealing. Due to moisture variations with depth, we model bare soil with a stratified dielectric profile with a rough surface on top. Small perturbation method (SPM) is used as the forward model. We use the full moisture profile for radar data synthesis and study the retrieval accuracy by varying the number of layers that represent the soil profile during inversion. The effect of measurement frequency on the accuracy of deep moisture retrieval is investigated. This work is intended for assessing the effect of subsurface profile on soil moisture retrieval from radar observations of NASA's Soil Moisture Active and Passive (SMAP) mission and future lower frequency airborne or spaceborne systems that may follow SMAP.