Microcotyle donavini has the general morphology of all species of Microcotyle, with a symmetrical body, comprising an anterior part which contains most organs and a posterior part called the haptor. The haptor is symmetrical, and bears 86 clamps, arranged as two rows, one on each side. The clamps of the haptor attach the animal to the gill of the fish. There are also two buccal oval suckers, septated, located at the anterior extremity. The digestive organs include an anterior, terminal mouth, a pharynx, an oesophagus and a posterior intestine with two lateral branches provided with numerous secondary branches. Each adult contains male and female reproductive organs. The reproductive organs include an anterior oval genital atrium, armed with numerous small spines, a medio-dorsal vagina opening at 750 µm from the anterior extremity, a single ovary and 18-22 oval testes which are posterior to the ovary. The eggs are fusiform, with a filament at each pole; one is short and thick.
