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.