ABSTRACT: Diatoms are responsible for a large fraction of oceanic and freshwater biomass production and are critically important for sequestration of carbon to the deep ocean. As with most surfaces present in aquatic systems, bacteria colonize the exterior of diatom cells, and they interact with the diatom and each other. The ecology of diatoms may be better explained by conceptualizing them as composite organisms consisting of the host cell and its bacterial associates. Such associations could have collective properties that are not predictable from the properties of the host cell alone. Past studies of these associations have employed culture-based, whole-population methods. In contrast, we examined the composition and variability of bacterial assemblages attached to individual diatoms. Samples were collected in an oligotrophic system (Station ALOHA, 22°45’N, 158°00’W) at the deep chlorophyll maximum. Forty eukaryotic host cells were isolated by flow cytometry followed by multiple displacement amplification, including 26 Thalassiosira spp., other diatoms, dinoflagellates, coccolithophorids, and flagellates. Bacteria were identified by amplifying, cloning, and sequencing 16S rDNA using primers that select against chloroplast 16S rDNA. Bacterial sequences were recovered from 32 of 40 host cells, and from parallel samples of the free-living and particle-associated bacteria. Bacterial assemblages varied substantially even among closely related host cells. Host cells and the free-living and particle-associated samples can be placed into distinct groups based on the phylogenetic relatedness of their associated bacteria, rather than the identity of the host cell. As yet, the functional implications of these groups are unknown.