Abstract
Climate change‐amplified extreme weather events are reshaping ecological communities globally. On coral reefs, heatwaves typically disrupt the obligate coral–algal symbiosis, with symbiont identity a prime determinant of coral resilience to these thermal extremes. Yet, whether heatwaves have long‐term effects on coral symbioses remains unclear due to a lack of longitudinal symbiont data. Here, we report on a decadal coral symbiont survey (2013–2023), spanning the most prolonged tropical marine heatwave on record (2015–2016) and its aftermath. Concomitant with mass coral mortality, we document wholesale transformation of the symbiont assemblages in two coral species, the legacy of which was persistent for 7 years post heatwave. We also found evidence suggestive of a symbiont's local extinction, of local human disturbance impeding symbiont recovery, and of new coral recruits hosting symbiont assemblages distinct from survivors. Our study demonstrates heatwaves can have long‐lasting impacts on symbioses raising concern for coral resilience to future heatwaves.