Critical to Atlantic sturgeon Acipenser oxyrinchus oxyrinchus recovery and monitoring is the ability to estimate abundance and identify age- and stock-specific threats to survival. As adult Atlantic sturgeon spend much of their lives broadly distributed in marine and estuarine environments, it is challenging to collect data needed to estimate these demographic parameters in the adult population. Alternatively, data collected from juveniles and subadults before emigration may be used to calculate indices of abundance and provide insights into recruitment dynamics and stage-specific survival. However, uncertainty about stock mixture during early life stages may limit the use of juvenile and subadult data for monitoring recovery. To better understand early life stage stock composition, we conducted a genetic mixed-stock analysis of over 500 juvenile and subadult Atlantic sturgeon captured in an overwintering area in the Hudson River, New York, USA, from 2017 to 2022. The majority of Atlantic sturgeon in our study were natal to the Hudson River population, regardless of sex, size, or age. As such, indices of relative abundance estimated from survey data are expected to primarily characterize the demographic trends of Hudson River juvenile and subadult Atlantic sturgeon. We also found a small proportion of individuals that were most likely to have originated from more distantly located rivers, highlighting the potential for long-distance migration in juvenile and subadult Atlantic sturgeon. Results of this study strengthen our understanding of juvenile and subadult Atlantic sturgeon habitat use in the Hudson River and improve our ability to use data from early age classes to monitor recovery and stage-specific survival.