There is a growing interest in the management of seamounts of the Southwestern Indian Ocean (SWIO) both in waters under national jurisdictions and in the Areas Beyond National Jurisdiction (ABNJ). New scientific knowledge has been gathered through various oceanographic cruises during the past decade, and new agreements are under consideration globally to promote conservation and sustainable use of the biodiversity in the ABNJ, where the deep sea ecosystems associated with seamounts are a growing matter of concern. SWIO seamounts have attracted the interests of fishers since the 1960s, and contracts for mining exploration have been granted recently. Seamounts are known to shelter rich, fragile and poorly resilient ecosystems whose important ecological functions are threatened by various anthropogenic pressures. Whereas many seamounts and shoals are located in national waters, many others fall in the ABNJ, with no current legal status per se. To ensure conservation of their habitats and biodiversity, it is essential that protection measures are instigated under an internationally recognized legal and institutional framework. In this paper, we review the current state of such a framework relevant to seamounts, with emphasis on fisheries and conservation in the SWIO. An emblematic seamount, the Walters Shoal, is selected as a case study to discuss how it could become a fully-protected space in the ABNJ. As a large part of the SWIO is under the mandate of the Nairobi Convention (as a Regional Sea under the auspices of UNEP), guidelines are proposed to encourage dedicated seamount governance within the framework of this Convention