Coral thermal tolerance is strongly influenced by the functional diversity of their photosymbiotic dinoflagellates. Yet, selection of Symbiodiniaceae for the use in coral research and restoration is largely based on genetic identity alone, providing limited insight into functional traits and stress tolerances. The Australian Institute of Marine Science (AIMS) maintains Australia’s largest and longest-standing collection of coral photosymbiont cultures, creating the requirement for throughout categorisation of available lineages. This project, therefore, incorporates a recently developed high-throughput phenotyping framework available at the National Sea Simulator to systematically characterise the functional traits and stress tolerances of 20 representative Symbiodiniaceae genotypes from the Great Barrier Reef. Monoclonal cultures were genotyped using ITS2 and LSU markers and then assessed for key traits (e.g. size, growth, photosynthetic performance, and thermal and light tolerance). Phenotypic measurements were assessed using flow cytometry and the innovative Phenoplate platform, enabling parallel assessment of photosynthetic parameters under controlled temperature and light gradients. By empirically linking genotype and phenotype, this research establishes a comprehensive catalogue which resolves variations in thermal tolerance within and among symbiont lineages of the Great Barrier Reef, exemplifying how interdisciplinary, operational phenotyping can translate mechanistic understanding into actionable tools for reef resilience under ocean warming.