As part of the Centre for Maritime and Regional Studies (CMRS) the Maritime Archaeology Programme is closely associated with a range of institutions in the fields of maritime archaeology and maritime heritage. Students benefit from the wide experience of these institutions and the opportunities they have to offer.

One partner of the CMRS is the Fisheries and Maritime Museum in Esbjerg. It is the largest institution of its kind in Denmark focusing on Danish fisheries, marine biology, the tidal wetlands (Waddensea), west Jutland coastal shipping and the North Sea offshore industries. It also has a substantial maritime library, which combined with the holdings of SDU, provides a large body of research material. The museum has an active shipwright who can assist researchers with ship reconstruction and construction techniques.

The centre for Marine Archaeology at Strandingsmuseum St. George is responsible for the archaeology of the Danish North Sea coast. The museum has a rich maritime collection and exibits the finds from the HMS St. George and HMS Defence wrecks.

Bangsbomuseet is responsible for the archaeology in Northern Danish waters. The museum has the well preserved Ellingå early medieval ship on display.

Langelands museum is responsible for the archaeology in central Danish waters. The museum pioneered maritime archaeology in Denmark, and has a long experience especially in submerged settlements.

The conservation laboratory in Ølgod has experience in the conservation of waterlogged materials from both submerged sites and shipwrecks, including the HMS St. George and HMS Defence wrecks.

The Viking Museum at Ribe also contributes to the program. The museum has more than 30 years of experience in wetland archaeology and waterlogged finds, and has an excellent record of international collaboration.

The National Museum. The department of archaeological Conservation in Brede is at the forefront of the conservation of archaeological material from submerged sites. The museum also develops methods for in situ conservation. The use of these methods is often of vital importance to the sustainable management of the underwater cultural heritage.

The Viking Ship Museum has made 'Roskilde' synonymous with maritime archaeology research at the highest international level.