Endolithic microflora were studied in recent scleractinian reef corals of Discovery Bay, Jamaica. Growing corals were collected at depths from sea level to 18 meters in the bay, forereef, and backreef. The inhabitants of coral genera Montastrea and Porites were selected for detailed study in each environment. The microborers, mainly endolithic green algae of the genus Ostreobium, were studied by means of SEM and thin sections. Thin-sections, the most successful technique, were made from horizontal and vertical sections of the coral skeletons. Filament counts were compiled for multiple transect lines in all samples. Montastrea skeletons contained many more filaments, possibly because their skeletons grow at slower rates than Porites. Algal filament variation within each species can be attributed to differences in coral growth rate, colony growth form, coral habitat, and depth. Although Ostreobium inhabits young corals, and grows and branches upward, only 47% of the specimens showed more filaments in the upper portions of the skeleton. Tiny filamentous tubes, within the skeletons were commonly still inhabited by microflora. The majority of corals studied contained green concentric algal bands within their skeletons. Counts substantiate that more algal penetrations, whether green with filaments or empty tubes, occur within these green bands. This fact suggests a correlation of greater numbers of algal filaments, green pigmented bands, and less dense skeletal material. Additional destructive and constructive evidence within the coral skeletons was present, and results from macroboring and encrusting organisms and incipient cementation.