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The Old Whaling site at Cape Krusenstern, Alaska, has been the subject of contested interpretations stemming from an original theory proposed by J. Louis Giddings more than half a century ago. In an attempt to address recent suggestions that the occupational history is more complex than originally believed, the site was the subject of a non-invasive geophysical survey conducted by our team in 2011. The project served as a starting point for assessing the potential for archaeological remains at the site that had not been detected with previous investigations, and to gain a better understanding of site morphology. The investigation was implemented with two well-established geophysical methods, ground-penetrating radar (GPR) and magnetic gradiometry. The survey revealed no unequivocal evidence of additional occupations as has been recently suggested, but did reveal a dynamic site morphology that may have implications for archaeological interpretation.