The algal cell wall is an important cellular component that functions in defense, nutrient utilization, signaling, adhesion, and cell-cell recognition — processes important in the cnidarian–dinoflagellate symbiosis. The cell wall of symbiodiniacean dinoflagellates is not well characterized. Here, we present a method to isolate cell walls of Symbiodiniaceae and prepare cell wall-enriched samples for proteomic analysis. Label-free liquid chromatography-electrospray ionization tandem mass spectrometry was used to explore the surface proteome of two Symbiodiniaceae species from the Great Barrier Reef: Breviolum minutum, and Cladocopium goreaui. Transporters, hydrolases, translocases, and proteins involved in cell-adhesion and protein-protein interactions were identified, but the majority of cell wall proteins had no homologues in public databases. We propose roles for some of these proteins in the cnidarian–dinoflagellate symbiosis. This work provides the first proteomics investigation of cell wall proteins in the Symbiodiniaceae and represents a basis for future explorations of the roles of cell wall proteins in Symbiodiniaceae and other dinoflagellates.