Flight initiation distance (FID), or the distance between a prey animal and an approaching intruder when the prey initiates its escape, is an important factor in wildlife management. We conducted a study on individually identified yellow-bellied marmots (Marmota flaviventris) to test 3 key assumptions of FID research: (1) differences in individual responses are small enough so as not to confound results; (2) pseudoreplication may bias results; and (3) habituation and sensitization can be studied without knowledge of individuals. We found that individual identity was not a significant predictor of FID. Furthermore, a moderate degree of pseudoreplication did not significantly affect the results of most analyses. However, individuals differed greatly in their rates of habituation, such that habituation was apparent only when individual identity was known and could not be detected without knowledge of individuals. If our marmot results can be generalized to other species, they suggest that researchers need not be concerned about individual identity when studying variables largely dependent on environmental factors, but that identification of individuals is important for studies of properties of individuals, such as habituation.