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In marine biology, many research fields are based on use of fish otoliths. All the studies dealing with otoliths need as starting point a perfectly clean otolith. Dissection is difficult when working on small or highly jagged otoliths. A common problem is that during otolith preparation some fish tissue may remain stuck to it, even after a mechanical cleaning. Then, supplementary cleaning with chemicals is needed. Classical methods are known to possibly alter otolith's structure and/or composition. Here, we present a chemical cleaning method using only sodium hydroxide. We have validated the method on two different fish species, Oblada melanura and Dicentrarchus labrax. Observation and analyses of morphological measurements have confirmed significant suppression of residual tissues. We propose this method as a good alternative to previously published mono‐ or multichemical methods.