ABSTRACTA thraustochytrid zoosporic fungus with characteristics of the genusSchizochytriumis a common member of an assemblage of different endolithic marine microorganisms found in carbonate shell fragments. We used clean shell fragments as bait in various subtidal marine locations on the coasts of Maine, Georgia and Jamaica. Heterotrophs (including fungi) were selected by covering each bait panel with a stainless steel shade that allowed sea water to circulate easily over the shell fragments. Shell fragments were recovered after six months. Details of the cytology of the endolithic organisms were revealed by a technique which produced a resin cast of the endoliths, or their traces, after fixed and embedded shells were decalcified. Scanning electron microscope observations were of the resin casts and transmission electron microscope observations were of sections of reembedded resin casts. Thraustochytrids were particularly abundant in fragments of mussel shells, which have more organic matrix than clam or oyster shells. Within the shells the thraustochytrids formed unusual elongated, tapered, and sometimes branched thalli that are divided into many vegetative cells, a characteristic feature ofSchizochytrium.The cell nearest the shell surface typically was a zoosporangium containing biflagellate zoospores. Ultrastructural evidence for the thraustochytrid nature of the endoliths included a layered wall of dictyosome-derived thin scales and the production of an ectoplasmic network from bothrosomes on the cell surface. This role of thraustochytrid fungi in bioerosion is new and unexpected.