The following subdivisions are active at the Institute of Baltic Region History and Archaeology of Klaipėda University:
- Archaeological Research Laboratory, founded in 2026. Headed by Tomas Rimkus;
- Underwater Research Centre, founded in 2003. Headed by Elena Pranckėnaitė;
- Centre for Conservation and Restoration, founded in 2020. Headed by Akvilė Poškienė.