The endosymbiotic relationship between cnidarians and photosynthetic dinoflagellate algae provides the foundation of coral reef ecosystems. This essential interaction is globally threatened by anthropogenic disturbance. As such, it is important to understand the molecular mechanisms underpinning the cnidarian-algal association. Here we investigated phosphorylation-mediated protein signaling as a mechanism of regulation of the cnidarian-algal interaction, and we report on the generation of the first phosphoproteome for the coral model organism Aiptasia. Using mass spectrometry-based phosphoproteomics in data-independent acquisition allowed consistent quantification of over 3,000 phosphopeptides totaling more than 1,600 phosphoproteins across aposymbiotic (symbiont-free) and symbiotic anemones. Comparison of the symbiotic states showed distinct phosphoproteomic profiles attributable to the differential phosphorylation of 539 proteins that cover a broad range of functions, from receptors to structural and signal transduction proteins. A subsequent pathway enrichment analysis identified the processes of 'protein digestion and absorption,' 'carbohydrate metabolism,' and 'protein folding, sorting, and degradation,' and highlighted differential phosphorylation of the 'phospholipase D signaling pathway' and 'protein processing in the endoplasmic reticulum.' Targeted phosphorylation of the phospholipase D signaling pathway suggests control of glutamate vesicle trafficking across symbiotic compartments, and phosphorylation of the endoplasmic reticulum machinery suggests recycling of symbiosome-associated proteins. Our study shows for the first time that changes in the phosphorylation status of proteins between aposymbiotic and symbiotic Aiptasia anemones play a role in the regulation of the cnidarian-algal symbiosis. This is the first phosphoproteomic study of a cnidarian-algal symbiotic association as well as the first application of quantification by data-independent acquisition in the coral field.