There is a growing interest in the management of seamounts of the South Western Indian Ocean (SWIO) both in waters under national jurisdictions and in the Areas Beyond National Jurisdiction (ABNJ). On the one hand, new scientific knowledge has been gathered through various oceanographic cruises during the past decade and, on the other hand, new agreements are under consideration globally to promote conservation and sustainable use of the biodiversity in the ABNJ, where the deep sea ecosystems associated to seamounts are a growing matter of concern. SWIO seamounts have attracted interests from fishing operators since the 1960s, while mining exploration contracts have been recently granted. Seamounts are known to shelter rich, fragile and poorly resilient ecosystems whose important ecological functions that are threatened by various anthropogenic pressures. While 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 institution 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. We select an emblematic seamount, the Walters Shoal, as a case study to discuss how this site could become a fully-protected space in the ABNJ. Since a large part of the SWIO is under the mandate of the Nairobi Convention (Regional Sea under the auspices of UNEP), guidelines are proposed to spur a dedicated seamount governance in the framework of this Convention.