Most scleractinian corals are under threat from global warming, yet some exhibit remarkable resistance to heat stress. Coral thermal tolerance depends on both the intrinsic properties of the cnidarian host and the physiology of their symbiotic algae (Symbiodiniaceae). Some corals adapt to heat stress by altering their Symbiodiniaceae communities, but these shifts are primarily observed over very short evolutionary timescales, leaving a gap in our understanding of coral holobiont evolution over longer periods. In this study, we combined ancient DNA analysis from a coral core with a metabarcoding approach to reconstruct past Symbiodiniaceae communities associated with a living colony of Porites lobata from New Caledonia over the last century. Using the SymPortal analytical pipeline, we identified 53 ‘defining intragenomic variants’ (DIVs) related to Symbiodiniaceae. The number of Symbiodiniaceae DIVs per sample ranged from 5 to 22 and showed no correlation with the age of the coraDNA sample or the total number of sequences obtained. Our results reveal a generally stable Symbiodiniaceae community associated with P. lobata, dominated by the C15 clade, though substantial shifts in community composition coincided with an extreme warm winter event. Additionally, we detected the presence of Azadinium spinosum (Dinophyceae) in two coraDNA replicates from the same position in the coral core, and sequences of the host P. lobata in a subset of samples. This study lays the groundwork for future research into the evolutionary dynamics of coral holobionts at the colony level across extensive temporal scales.