Mussels in the genus Bathymodiolus host endosymbiotic bacteria in their gills, from which the mussel derives much of its nutrition. Bathymodiolin mussels also have functional digestive systems and, as in shallow-water mytilid mussels, cells of the digestive diverticulae are of two types: basophilic secretory cells and columnar digestive cells. Cellular contents of secretory and digestive cells of Bathymodiolus thermophilus and Bathymodiolus brevior from deep-sea hydrothermal vents are comparable to cellular contents of these cell types observed in shallow-water mytilids. In the seep mussel Bathymodiolus heckerae, cellular contents of columnar cells were anomalous, being dominated by an unknown cellular inclusion herein called spherical inclusion unknown or SIX. SIX was observed in all digestive cells and some basophilic cells of B. heckerae examined with TEM. It is a large (2–10-μm diameter) and abundant (7 ± 1.5 inclusions per epithelial cell section) inclusion, with a double external membrane and stacked internal lamellae. No microbial DNA was detected in digestive tubules of B. heckerae using molecular probes, preferential DNA amplification techniques, or DAPI staining, suggesting that SIX is not a unicellular parasite or symbiont. The ubiquity and abundance of SIX within cells of the digestive diverticula suggest that it has an important cellular function (positive or negative), yet to be determined.