He is an evolutionary ecologist and geneticist, known for his research on host–pathogen interaction and coevolution, mainly using the model system Daphnia and its parasites.

In 1992 Ebert joined the research group of William (Bill) Hamilton at the University of Oxford, where he started to work on host - parasite interactions.

He did a further postdoc in the NERC Centre for Population Biology (CPB) at Silwood Park with John Lawton, before he became Assistant professor at the University of Basel, Switzerland.

This summer school was launched by Stephen Stearns in 1987, and had featured an outstanding selection of evolutionary biologist on its faculty, including John Maynard Smith, Georg Williams, W. D. Hamilton, Richard Lenski and Peter and Rosemary Grant.

[18] Dieter Ebert is a member of the Academy of Sciences Leopoldina,[19] the European Molecular Biology Organization (EMBO),[20] and is a permanent fellow of the Berlin Institute for Advanced Study[21]