SWIMS was originally named as The Swire Marine Laboratory and was comprised of an academic and residential block. The laboratory was built with a donation from The Swire Group of Companies and was formally opened by Sir John Swire in November 1990. This facility provided basic laboratory and living space for research students and staff, especially for research conducted within the surrounding shores of the Cape d'Aguilar peninsula.

In 1991 the Cape d'Aguilar area was designated a Site of Special Scientific Interest (SSSI) in recognition of the growing interest in understanding and conserving Hong Kong's marine environment. To contribute towards this need, the laboratory was extended in 1994 to increase its laboratory and residential capacity. This included extending the lower laboratory, adding a further suite of rooms to the first storey (including a new Reference Museum), extending the seminar room and diving facilities, and building a new residential block. This expansion was supported, again, by a generous donation from The Swire Group Charitable Trust and, in recognition of its growing importance, the laboratory was renamed The Swire Institute of Marine Science (SWIMS).

The new facility was opened in November 1994 by Sir John Swire, HKU's Vice Chancellor Prof. Wang Gungwu, and Prof. Qu Geping from China. The increasing importance of marine research, and specifically the area around the SWIMS was further recognized with the designation of Cape d'Aguilar as Hong Kong's first, and to date only, Marine Reserve in 1996.

SWIMS continued to develop and expand in subsequent years. In 2003, with contributions totaling $8 million from The University of Hong Kong and The Swire Group, SWIMS underwent an extensive renovation and was officially re-opened on 3rd December 2003. The renovation included a new design and complete refitting of the laboratory which is primarily intended for postgraduate research. This new, modern laboratory has created more effective use of bench space and a re-organization of large items of equipment, whilst maintaining the open, natural light and views of the bay. In addition, an extensive upgrade on the seawater aquarium with the provision of new cyclone and sand filters has considerably improved the water quality, which means a wide range of marine organisms can now be reared in good conditions in a series of outdoor tanks. The indoor aquarium area has also been re-designed to provide an extremely flexible variety of facilities.

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