We conducted time series sampling of individual tagged colonies of common corals in St. John, US Virgin Islands, and analyzed their symbiotic algae (Symbiodiniaceae) by ITS2 metabarcoding. Seventy-five corals from 9 species were marked and sampled in 2017. Of these colonies, 41% were sampled in 2018, and 72% in 2019 28% could not be found and were assumed to have died. Symbiodiniaceae ITS2 sequencing identified 525 distinct sequences (comprising 42 ITS2 type profiles), and symbiont diversity differed among host species and individuals, but was in most cases preserved within hosts over 3 yrs that were marked by physical disturbances from major hurricanes (2017) and the regional onset of stony coral tissue loss disease (2019).