There is at present a ‘coral reef crisis’; one of the more drastic consequences of this is a phase shift, in which reef-building corals are replaced by non-reef building benthos such as macroalgae and soft corals. Previous studies have principally focused on the shift to macroalgae. Our goal was to investigate whether the dominance of the zoanthid Epizoanthus gabrieli on some reefs of Todos os Santos Bay, Brazil, represented a non-algal phase shift. In 2003, we identified a high cover of this species on two reefs (52% and 70%), but only in 2007 was it possible to confirm a reduction in coral cover. This dominance has persisted for over 9 years, characterizing a true phase shift. This loss of coral cover may be a result of anthropogenic disturbances within the bay; however, given the large number of human impacts, further studies are needed to identify specific causes of this shift. Although there are some reports of phase shift involving species pertaining to the Class Anthozoa, this is the first report of this phenomenon involving the order Zoanthidea.