Characterizing the molecular interface between the host and symbiont is critical for understanding cnidarian-dinoflagellate symbiosis. While numerous proteins involved in the regulation of symbiosis have been identified in cnidarian hosts, comparatively little is known for the dinoflagellate symbionts. Despite ample evidence that symbionts undergo a variety of molecular changes after establishing symbiosis in hosts, thus far, only a few symbiosis-specific symbiont proteins have been characterized. In this study, we developed DNA aptamers as a novel molecular tool to study symbiosis-specific proteins. DNA aptamers are single-stranded oligonucleotide probes that bind with high affinity and specificity to ligands. Aptamer development requires no a priori knowledge of their targets, and unlike antibodies, custom aptamer development is affordable and can be synthesized in a standard molecular laboratory. For our application, we used the model system sea anemone, Aiptasia, and its symbiont, Breviolum minutum, as selection targets for aptamer development. Using a procedure known as Cell-SELEX (Selective Evolution of Ligands by Exponential Enrichment), we generated aptamers that are specific to B. minutum in the symbiotic state, but not the free-living state. Generated aptamers can be used in live fluorescence imaging, discovery of symbiosis-specific proteins, and studying protein function. The introduction of Cell-SELEX and the DNA aptamer toolkit will allow new approaches for the study of cnidarian-dinoflagellate symbiosis, and examples of such applications will be presented.