Summary The presence of photosynthetic zooxanthellae (Dinoflagellates) in the tissue of many cnidarians is the main reason for their ecological success (i.e. coral reefs). It could also be their demise, as worldwide reef building coral bleaching is nothing less than the breakdown of this symbiotic association. The stability of this relationship is then the principal marker for the biomonitoring of the cnidarian health. We have therefore developed a new, simple method to isolate zooxanthellae in few steps using a NaOH solution. The protocol was validated in three symbiotic cnidarian species: a sea anemone, a gorgonian and a coral. Our method allows the isolation of intact and viable zooxanthellae with better yields than classic methods, especially for species with calcareous skeleton. Moreover, the isolated zooxanthellae were free of host contaminants, facilitating subsequent specific molecular analyses.