The Department of Molecular Biology was founded in the University of Edinburgh in October 1965 by Martin R Pollock, Head of the Division of Microbial Physiology, and William Hayes, Director of the MRC Microbial Genetics Research Unit. Pollock and Hayes had realised that the fields of biochemistry and molecular genetics had converged to the extent that a new department combining them would be able to make significant contributions to the field. Several Universities were considered and Edinburgh eventually chosen.

They were initially based in the biophysics unit but moved into the Darwin Building in 1968. At this point, the staff of the MRC Microbial Genetics Research Unit which had been based in London moved into the department. The first PhD students joined in 1965, third year courses began in 1968 and the first honours courses began in 1969. The department's policy was that their honours students should go elsewhere to study for a PhD.

The department was involved in a lot of research which included recognition of bidirectional transcription of DNA in E. Coli, progress in the elucidation of the genetics, physiology and structure of factors responsible for antibiotic resistance in bacteria, the first bacteriophage vectors for recombinant DNA technology and their application to the cloning and manipulation of genes from any organism, the application of the methods of Molecular Biology to explore the possibilities of malaria vaccines and the production of the first artifical vaccine for Hepatitis B. These were produced by Ken Murray and the proceeds partly used to found The Darwin Trust.

The Darwin Trust founded the Biocomputing Research Unit to enable the department to cope with the enormous expansion in the flow of information regarding amino acid and the nucleotide sequences that underpin all genome projects and also founded a unified Science Library.

Other departments dealing with different aspects of biology were scattered across the university and plans were made to pull these strands together. In 1990 the department ceased in that form and became part of the Institute of Cell and Molecular Biology.