The mass bleaching of corals that occurred on the Great Barrier Reef (GBR), Australia, in early 1998 was one of the most severe on record. There is surprisingly little known about the fate of bleached corals, which may either regain their zooxanthellae and recover, or may die, in which case they generally become overgrown by algae. The nature and dynamics of this algal overgrowth and its effects on the corals are not well understood. In this study we describe the composition and time-course of algal recruitment on bleached corals, and the possible roles of that recruitment on the fate of the corals, at 2 inshore reefs of the GBR. Massive Porites spp. corals were selected with different degrees of bleaching, and the cover of live coral tissue, and relative abundance and composition of algal recruitment were followed in small plots over 2.5 yr. The bleaching disturbance precipitated a major shift in abundance of corals and algae. All dead corals were colonised by a diverse community of epilithic and endolithic algae, the nature and composition of which was variable and related to the stage of the succession, the severity of bleaching and reef location. Quantitative data on species composition of colonising algae are given, and are apparently the first such data. The epilithic algal assemblage was initially dominated by diatoms and blue-green algae, but rapidly shifted to an assemblage dominated by upright and branched filamentous algae (e.g. Polysiphonia spp., Hincksia mitchelliae, Sphacelaria spp.) and, on 1 reef, fleshy macroalgae (e.g. Asparagopsis taxiformis, Sargassum spp.). Endolithic algal assemblages were largely dominated by the green algae Ostreobium spp. and cyanobacteria. Algal colonisation on clay settlement plates was distinctly different from that on dead coral skeleton. Algal colonisation was not the initial cause of coral tissue mortality, although it may have contributed to the failure of corals to recover after bleaching. The results thus emphasise the role of coral disturbances and substratum availability in controlling abundance of coral reef benthic algae, in contrast to ‘bottom-up’ and ‘top-down’ views that assume changes in algal abundance are the major cause of changes in coral abundance. The considerable variability in the outcome of bleaching damage and algal colonisation demonstrates the potential for major and variable effects on the recovery of coral populations, with implications for the future reef status.