A need exists for additional methods to examine cnidaria at the cellular level to aid our understanding of health, anatomy, and physiology of this important group of organisms. This need is particularly acute given that disease is emerging as a major factor in declines of ecologically important functional groups such as corals. Here we describe a simple method to process cnidarian cells for microscopic examination using the model organism Aiptasia. We show that this organism has at least 18 cell types or structures that can be readily distinguished based on defined morphological features. Some of these cells can be related back to anatomic features of the animal both at the light microscope and ultrastructural level. The cnidome of Aiptasia may be more complex than what is currently understood. Moreover, cnidarian cells, including some types of cnidocytes, phagocytize cells other than endosymbionts. Finally, our findings shed more light on morphologic complexity of cell-associated microbial aggregates and their intimate intracellular associations. The tools described here could be useful for other cnidaria.