Numerous seabird and marine mammal species occur in the subtropical and subantarctic zones of the southern Indian Ocean region. They breed, moult and rest at French, South African and Australian islands in the region and forage at sea in the Exclusive Economic Zones of these nations, the Convention Area, and Areas Beyond National Jurisdiction. Information on the at-sea distribution of these species is important for understanding ecosystem processes and patterns in the region, and is a key component of any spatial conservation and management frameworks. Information on the distribution of marine predators is widely used to define priority areas for conservation and management, including several such initiatives in the extended Southern Ocean. Seabird and marine mammal distribution has been studied mainly using two methods: animal-borne biotelemetry/biologging and at-sea sightings records. Here, we give an overview of data on the distribution of marine mammals and seabirds–collected mainly through long-term programmes at French and South African islands–with the aim of identifying data sources that can inform pelagic ecoregionalisation to support spatial conservation and management planning in this region. We identify priorities for further distribution data collection related to life-history stages, sites and species and we identify broader challenges for understanding marine predator distribution process and pattern in this region, towards spatial conservation and management planning.