Professors at ZMT are appointed jointly with universities (University of Bremen and Jacobs University Bremen) as so-called cooperation professorships. Students at ZMT receive their academic degrees mainly from these universities.

Aside from the doctoral programme one particular focus in ZMT education is placed on the Master study programme ISATEC (International Studies in Aquatic Tropical Ecology) for German and international students which is offered in close collaboration with the University of Bremen. Both institutions jointly coordinate the programme with ZMT also contributing to teaching ISATEC courses.

Participants are trained in theoretical and applied ecology, resource evaluation, and the foundations of socio-economics. The programme maintains a focus on concepts for the protection and sustainable management of tropical coastal ecosystems. In addition to theoretical and technical components, there is also an emphasis on the importance of cooperative multi-cultural group work within the course and thesis components of the programme.

Furthermore, ZMT also organises summer schools (particularly in its partner countries) and offers special courses for example in research diving.