We tested an a priori plant community classification model, developed using topographic characteristics and GIS, to determine if it could be used to predict the distribution of the endangered Carolina northern flying squirrel (Glaucomys sabrinus coloratus) in the Balsam Mountains of western North Carolina. Nest boxes were used to sample northern flying squirrel populations in areas of predicted presence versus areas of predicted absence. There was no difference between the two site types for presence or absence of northern flying squirrels. However, significant differences were found for number of squirrels captured and nest boxes used between types. The mixed results of our analyses suggested that our definition of predicted present and predicted absent sites was flawed. Northern flying squirrels were present in spruce/northern hardwood ecotones (predicted present), however they were also present in low densities in spruce/red oak ecotones (predicted absent), though only in portions of the ecotone dominated by spruce. Landowners and managers can utilize the model to help predict whether northern flying squirrels occur, however it should not be used as the sole discriminator.