In developing regions, coastal communities are particularly dependent on small-scale fisheries for food security and income. However, information on the scale and impacts of small-scale fisheries on coastal marine ecosystems are frequently lacking. Large marine vertebrates (marine mammals, sea turtles and chondrichthyans) are often among the first species to experience declines due to fisheries. This paper reviews the interactions between small-scale fisheries and vulnerable marine megafauna in the southwestern Indian Ocean. We highlight an urgent need for proper documentation, monitoring and assessment at the regional level of small-scale fisheries and the megafauna affected by them to inform evidence-based fisheries management. Catch and landings data are generally of poor quality and resolution with compositional data, where available, mostly anecdotal or heavily biased towards easily identifiable species. There is also limited understanding of fisheries effort, most of which relies on metrics unsuitable for proper assessment. Management strategies (where they exist) are often created without strong evidence bases or understanding of the reliance of fishers on resources. Consequently, it is not possible to effectively assess the current status and ensure the sustainability of these species groups; with indications of overexploitation in several areas. To address these issues, a regionally collaborative approach between government and non-governmental organisations, independent researchers and institutions, and small-scale fisheries stakeholders is required. In combination with good governance practices, appropriate and effective, evidence-based management can be formulated to sustain these resources, the marine ecosystems they are intrinsically linked to and the livelihoods of coastal communities that are tied to them.