Concern over illegal, unreported and unregulated (IUU) fishing has led to a number of policy, trade and surveillance measures. While much attention has been given to the impact of IUU regulation on industrial fleets, recognition of the distinct impacts on small‐scale fisheries is conspicuously lacking from the policy and research debate. In this paper, we outline three ways in which the application of IUU discourse and regulation undermines small‐scale fisheries. First, the mainstream construction of “illegal,” “unreported” and “unregulated” fishing, and also the categorical use of “IUU” in an all‐inclusive sense, disregards the diversity, legitimacy and sustainability of small‐scale fisheries practices and their governing systems. Second, we explore how the recent trade‐related measures to counter IUU fishing mask and reinforce existing inequalities between different sectors and countries, creating an unfair burden on small‐scale fisheries and countries who depend on them. Third, as IUU fishing is increasingly approached as “organized crime,” there is a risk of inappropriately targeting small‐scale fisheries, at times violently. Reflecting on these three trends, we propose three strategies by which a more sensitive and ultimately more equitable incorporation of small‐scale fisheries can be supported in the global fight against IUU fishing.