A process is claimed for decapsulating crustacean or rotifer eggs wherein the outer shells of the eggs are removed by dissolving the outer shells of the eggs by means of a liquid medium containing permanganate. The decapsulation process can be either performed under conditions which are lethal for the eggs or under non-lethal conditions which enable to obtain viable decapsulated eggs. The advantage of decapsulating cysts with permanganate instead of with hypochlorite, which is the known decapsulation process, is that this process is practical to implement on a large scale in which it is not hampered by pollution caused by the chemicals incorporated in the process nor the environmental concerns that are raised for the disposal of such chemicals. This advantage can also be achieved by an alternative process which involves the step of dissolving the outer shells of the eggs in a liquid medium having a pH higher than 11 and a temperature higher than 600 C and/or which contains persulfate.