© 2019 Inter-Research. All Rights Reserved. White sharks Carcharodon carcharias and shortfin mako sharks Isurus oxyrinchus are globally distributed apex predators and keystone species. However, regional information regarding juvenile biology, such as habitat preferences and trophic ecology, is lacking. This study investigates habitat use and feeding ecology of juvenile shortfin mako and white sharks in an aggregation site with high catch of these species by artisanal fisheries in Sebastian Vizcaino Bay (SVB; Baja California, Mexico) using stable isotope analysis (SIA) of carbon (13C) and nitrogen (15N). During 2015 and 2016, we collected muscle samples from newborn, young of the year, and juvenile shortfin mako and white sharks from individuals with similar body size, as well as local prey, to develop a conceptual foraging framework based on SIA. We found a positive relationship between shortfin mako length and 15N values, indicating ontogenetic changes in diet based on prey or locality. Bayesian isotopic mixing models (MixSIR) using prey from different regions in the North Eastern Pacific suggested diet shifts in shortfin makos from offshore, northern habitats to inshore habitats of southern Baja (e.g. SVB), while analysis of white sharks reflected use of inshore habitats of both southern California, northern Baja, and SVB. Our results suggest shared resource use between these shark species and potentially high consumption of prey from SVB and other similar coastal regions in southern Baja. This study characterizes high use of inshore regions for juvenile shortfin mako and white sharks, which has important implications for management and conservation practices.