Camouflage via animal coloration and patterning is a broadly important antipredator strategy. Behavioral decision making is an influential facet of many camouflage strategies; fitness benefits often are not realized unless an organism selects suitable backgrounds. Controlled experimental studies of behavioral strategies in selection of backgrounds conferring camouflage, however, are rarely paired with observations of wild populations. In order to investigate how substrate composition influenced habitat preference and selection by juvenile desert tortoises (Gopherus agassizii), we completed a manipulative experiment in captivity and an observational study in the wild. In our captive experiment, we found that tortoises spent a greater portion of their time near rocks. We similarly found that wild tortoises preferentially placed themselves in areas with equivalent or larger-sized rocks. Additionally, juvenile tortoises were found to be less detectable on rock substrate by observers than they were on substrate-lacking rocks. We hypothesize that rocks improve juvenile tortoise camouflage and thus that tortoises select for habitat containing rock substrate, in part, due to a survival advantage conferred by such use. The desert tortoise is a threatened species, and the present study provides a model for examining the intersection between behavior and conservation, with implications for how suitable habitat is defined and measured in species conservation programs.