In 1999, an unregulated orange roughy fishery emerged in the high seas of the South West Indian Ocean. In response to this development, discussion began with key players, including New Zealand, on the establishment of a regional fisheries management arrangement. Parallel to these discussions, negotiations were taking place between east African coastal States on a draft Agreement to establish a South West Indian Ocean Fisheries Commission (SWIOFC). In 2001, it became clear that the two processes should be linked and the first consultation to establish a SWIOFC, including for high seas demersal fishery resources, took place. At the third consultation in January 2004, it was agreed that the interests of developing coastal States for cooperation and development in relation to fisheries within Exclusive Economic Zone jurisdictions would be progressed separately from interests in the high seas fisheries. A separate high seas agreement would therefore be negotiated.

The SIOFA aims to establish a legally binding framework to manage the demersal species in the high seas areas of the South Indian Ocean. The objectives of the agreement are to ensure the long term conservation and sustainable use of the fishery resources in this area and to promote sustainable development of fisheries taking into account the needs of developing states bordering the region and a Party to the agreement. The agreement provides mechanisms for the Meeting of Parties to adopt legally binding conservation and management measures to achieve those objectives that contracting parties will be required to implement and enforce.