MBI was established in 1997 when the University of Bergen decided to create a new Department of Molecular Biology at the Science Faculty (Det matematisk-naturvitenskapelige fakultet).
The new department was established with staff from Laboratory of Biotechnology (FLB), Department of Biochemistry and Molecular Biology (IBMB) and the Laboratory for Marine Molecular Biology (LMM). The new Department was located to the High Tech Centre at Marineholmen, and was fully operational from January 1997. The first Head of Department was prof. Dag E. Helland, followed by prof. Rune Male and prof. Anne Marie Szilvay.
When the Science Faculty was reorganized in 2004, MBI remained a separate department and prof. Johan R. Lillehaug was appointed Head of Department.