Modern environmental research is typically governed by a number of protocols designed to embrace the epistemological and ethical values of society. These protocols evolve in response to changing values, and few disciplines in environmental science have received as much attention as biological conservation. This paper describes the events leading to a controversy regarding a particular research technique used to investigate the cause of a long-term population decline of southern elephant seals (Mirounga leonina) at Macquarie Island, south of Australia – hot-iron branding of individuals. We discuss procedures and protocols that were in place at the time the controversy erupted, the subsequent reflection of the researchers and authorities involved, and the steps taken to avoid future occurrences. Our treatment of the issue is framed within a discussion of modern ethical philosophy, and our aim is to identify the true source of the controversy. We offer several suggestions as to how such events can be avoided in the future, and provide a model framework for incorporating changing ethical values into important biological conservation objectives.