The collection represents the variety of fauna of the Baltic Sea and the global ocean. In major, the collection consists of dry-preparations of sea animals. Counting 25 000 exhibits, the collection presents shells, corals, crustaceans, echinoderms, mammals, birds, fishes, fossils of sea animal. 

The collection of sea shells has been accumulated since 1975. Presently counting 23000 shells brought to the Museum from various parts of the global ocean, the collection is one among the best collections in Europe. The shells were collected during the scientific expeditions, last ones arranged to New Caledonia (the Pacific Ocean) in 1995 and to Tahiti (French  Polynesia, the Pacific Ocean) in 1997. 
In 2002, the collection was supplemented with 5000 shells by a private collector Feliksas Rimkevičius; in 2007, 2014 shells of Gastropoda were received from a private collector Henrikas Danila. In 2014, the Museum obtained a numerous collection of murexes including 1113 items. 
The main purpose of the collection is to disseminate the scientific information to the professionals, to educate the wide public, students and school children. The collection is presented in the permanent exhibition of the Museum, temporary mobile exhibitions, and the LIMIS.