Attention has been given in recent years to the topic of international fisheries governance and the drivers of illegal, unreported and unregulated (IUU) fishing. Issues relating to Flag State responsibility and the use of ‘flags of convenience’ (FoCs) or ‘flags of non-compliance’ (FoNCs) have been prioritized by international organizations seeking solutions to the problems that currently plague the high seas. To fully address these problems, it is necessary to develop concise and relevant operational definitions. Here, the international fishing fleet has been characterized using categories that describe differing flag use behaviors. Behaviors most associated to IUU activity were also identified through classifying an official list of IUU vessels using these same definitions. Flagging behaviors were found to differ between the subset of IUU vessels and the global fleet of fishing vessels examined. In particular, vessels flying flags of States exhibiting consistent patterns of failure in compliance with international obligations, defined here as ‘flags of non-compliance’ (FoNCs); vessels flying flags of States that did not match the State of vessel owner control or residence, defined here as ‘flags of convenience’ (FoCs); and vessels for which limited information was available on ownership, flying flags defined here as ‘flags of unknown affiliation’ (FoUAs) were more common within the group of IUU-listed vessels. In seeking solutions relating to the prevalence of IUU fishing, focus should be given to improving our understanding of the underlying drivers and incentives motivating vessel owners to engage in these flag use behaviors more closely associated to IUU activities.