This paper explores the challenge of respecting the local nature of traditional knowledge in two Pacific Islands’ regional initiatives. It argues that the embedded nature of traditional knowledge within the social fabric of Pacific Island communities necessitates an approach to regulation that respects existing customary laws and institutions, and contrasts this with the prevailing state-centred approaches. It also unpacks the different agendas behind the ambiguous term ‘protection’ and demonstrates the potential for misunderstanding among different stakeholders involved in this field. The paper finally identifies a number of negative consequences that could eventuate if a homogenised, state-based approach is adopted in this area, arguing that care must be taken to ensure that the regulatory framework chosen does not destroy more than it protects.