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Dark coloration of coral skeleton forming black bands is commonly observed in fractured, massive-coral colonies (Porites lutea and P. lobata) collected from Mayotte Island in the Mozambique Channel and Moorea Island in French Polynesia. Black-banding was similar in corals from the two areas and was associated with an assemblage of microbial endoliths: Ostreobium queketti, a common siphonal chlorophyte, and a type of Aspergillus-like fungus. Fungi of coral skeletons are capable of euendolithic growth entirely within the skeleton, and of cryptoendolithic growth whereby they spread from the skeleton into the skeletal pores. The morphology and size of fungal hyphae differs significantly between euendolithic, cryptoendolithic and reproductive phases. Reproductive phases involve formation of conidiophores. Insoluble residues in black bands involve a dark pigment and a dark membranous veil. When attacked by fungi, the algae are usually destroyed. They darken and are threaded by dense, dark-brown, fibrous excrescences. The fungi excrete a dark pigment that stains the surrounding skeletal carbonate black. The pigment is organic, and its presence correlates with higher concentrations of polysaccharides. Black bands match high-density bands of the coral skeleton. Both black bands and high-density bands form at the end of the rainy season in Mayotte. Thus, black-banding in the corals studied is caused by a series of events, beginning with an increase in the abundance of endolithic algae followed by an increase in skeletal density. The algae are then attacked by fungi, which produce more cryptoendolithic hyphae and conidia that are associated with production of the dark pigment.