California hazelnuts (Corylus cornuta var. californica) are abundant in the archaeological record of site CA-SMA-113 in Quiroste Valley Cultural Preserve, and hazel management on the Central Coast was recorded in late 18th century Spanish accounts. However, this species is currently absent from Quiroste Valley proper and rare in the watershed, though it is locally common elsewhere in the Santa Cruz Mountains. Because high California hazelnut abundance is associated with frequent fire regimes, we believe that its current low abundance could be due to fire suppression enforced in the region for the past two hundred years. We sequenced nuclear microsatellites from ten populations of California hazelnuts to test the hypothesis that this species has experienced demographic changes in response to changing climate and land management practices. We found that all populations exhibited high levels of genetic variation and negative population growth consistent with large population sizes in the past with some decline over time. We also found subtle patterns of geographic structure suggesting that Quiroste Valley and neighboring Butano may have been important refugia habitats during past climate warming events. These results provide an important foundation demonstrating that population genetic approaches can be applied to eco-archaeological research on indigenous landscape management and set the stage for future work using genetics to reveal further details of the demographic history of Quiroste Valley hazelnut populations.