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Sonoran Desert Tortoise (SDT; Gopherus morafkai) populations face threats from habitat loss and fragmentation. Effective management of SDTs in Arizona will require an understanding of the species’ age-related habitat needs; however, no published research addresses habitat selection and use in juvenile SDTs. We investigated microhabitat selection of juvenile SDTs in the Mazatzal Mountains in central Arizona. Eleven juvenile SDTs were tracked with radiotelemetry from April 2010 to December 2011. To determine habitat selection, we compared microhabitat characteristics from 117 tracked-tortoise locations to an equal number of random locations during 2 seasons. The summer monsoon (July to September) was the season of greatest SDT activity, whereas winter (December to February) was a season of relative inactivity and hibernation. We found that juvenile SDTs selected enclosed shelters on rocky hillsides with high proportions of boulders and annual vegetation during summer monsoon, and enclosed shelters on steep slopes with a high amount of leaf litter during winter hibernation. Microhabitat selection by juvenile SDTs allowed us to develop a habitat suitability model in a geographic information system (GIS); our model correctly predicted 82% of juvenile tortoise locations in suitable habitat at our site. Results from this study, the first of its kind in the Sonoran Desert, identify key habitat features selected by juvenile SDTs in central Arizona and provide a framework to develop GIS tools to predict juvenile tortoise habitat.