The Department of Molecular Ecology headed by Rudolf Amann analyzes the diversity, composition, and function of marine microbial communities by applying and developing tools of molecular biology. Techniques such as comparative sequence analysis including genomics and metagenomics, fluorescence in situ hybridization, confocal laser scanning microscopy and flow cytometry are used to study symbioses, bacterioplankton, and benthic microbial communities.

The department is structured into three groups.
The Microbial Genomics group headed by Frank Oliver Glöckner, the Symbiosis group headed by Nicole Dubilier, and the core group Molecular Ecology.

Three senior postdocs support the head of the department in running distinct research projects:
(i) Bernhard Fuchs, bacterioplankton & flow cytometry
(ii) Katrin Knittel, benthos & CLSM
(iii) Anke Meyerdierks, metagenomics.