A study was conducted to characterize the assemblages of invertebrate endofaunal organisms that live in association with the sessile epifauna inhabiting live-bottom reefs at the Gray's Reef National Marine Sanctuary (GRNMS) off the coast of Georgia. Epifaunal hosts were collected in May 2005 from areas described previously as containing densely colonized, live-bottom habitat. A subset of 24 hosts, consisting of three individuals from each of three sponge species (Ircinia felix, Ptilocaulis walpersi, and Axinella polycapella) and five individuals from each of three octocoral species (Leptogorgia hebes, L. virgulata, and Titanideum frauenfeldii), were selected for analysis in the present study. The 24 hosts examined contained a total of 132,056 solitary and 61 colonial associates, belonging to 115 taxonomic groups. Densities of endofauna were very high as compared to endofaunal densities in other areas. An analysis of similarity indicated that the composition of endofaunal associates between the two host groups were significantly different and a cluster analysis revealed further endofaunal differences among host species and morphological types. It is clear from this study that epifaunal sponges and octocorals at GRNMS provide important habitat for abundant and diverse assemblages of associated endofauna. Also, as these assemblages appear to vary among hosts, it is apparent that a thorough characterization of these endofauna for a specific ecosystem would benefit from the analysis of multiple host species.