The Great Reef of Toliara, on the southwestern coast of Madagascar, has been documented as harbouring flourishing reef communities in the 1960s, but has since been affected by various threats, causing a coral decline last reported in 2008. In 2017, we examined the spatial heterogeneity in coral community structure in the region of Toliara. Coral assemblages were characterized by a marked spatial variability, with significant variation for most of the descriptors among the three major habitats and also among stations within habitats. We recorded high coral cover, with values >40% at six of the 10 stations, which was associated with high abundance of coral colonies. We also documented the return to an Acropora-dominated coral assemblage. While these positive results suggest a recent return to healthier coral assemblages, they must be tempered, as the diversity that we recorded was lower than in the 1960s. Moreover, we found a high cover of algae at several stations, suggesting that the ecosystem is likely close to the tipping point toward a phase shift. Finally, the population size-structure of major coral taxa was positively skewed, with few large colonies to ensure the replenishment of local populations. The marked spatial variation suggests that marine protected areas should integrate a sufficiently large area to capture the scale of this spatial heterogeneity.