Between 1962 and 2003 significant coral species changes within reef assemblages at Todos os Santos Bay (TSB), Bahia (Brazil) have taken place, following what appears to have been a 400 year contraction of coral reefs from the inner, landward reaches of the bay. The last 40 years in particular encompassed rapid and extensive urban and industrial development its surrounding lands, which contributed to coral reef changes. However, changes in this environment have influenced coral reef resilience since the arrival of the Portuguese in the XVI century, creating knock-on effects that modified and simplified coral reef ecosystems in the bay. Clues to the limits of coral resilience may be found in natural and human disturbance regimes to which the corals have been subjected in the past, and for that reason we listed and categorized what little is known about Holocene and historical conditions in TSB, proposing alternatives for a resilience management of the bay.