The sea anemone Exaiptasia diaphana (Aiptasia) is a versatile model in studying cellular mechanisms that govern cnidarian-Symbiodiniaceae symbiosis, the foundation of coral reef ecosystems. Here, we provide a protocol to efficiently dissociate adult Aiptasia tissue into a single-cell suspension using enzymatic digestion. We detail steps including washing animals, dissociating tissue with pronase digestion, and evaluating dissociated single cells using fluorescence imaging. This procedure can be applied to other cnidarians, including coral polyps. For complete details on the use and execution of this protocol, please refer to Jinkerson et al. (2022).1.