Perennial pepperweed is an invasive plant species that occurs throughout the western United States. This study develops a predictive model for perennial pepperweed distribution for the San Francisco Bay Area, based on spatial variables. Distribution data were developed by mapping perennial pepperweed along the shoreline of the South San Francisco Bay, using geographic positioning system units. Spatial relationships between its distribution and spatial variables were tested using binomial logistic regression. Predictive models were mapped using geographic information systems (GIS), and high risk areas within the San Francisco Bay Area were identified. Perennial pepperweed was found to occur within marsh habitats with full tidal action and near open water. This study demonstrates that habitat variables from widely available GIS layers can be used to predict distribution patterns for perennial pepperweed. The model results were compared to land ownership within the study area to demonstrate a management application of the model.