The current study examined instream habitat associations among 1 common and 3 federally threatened mussel species at 3 sites in a southeastern watershed (Choctawhatchee River). We documented instream habitat structures (e.g., leaf pack, root mat, root wad, woody debris, and log) in the immediate vicinity (∼5 cm) of 94 Elliptio pullata (Gulf Spike), 263 Pleurobema strodeanum (Fuzzy Pigtoe), 117 Fusconaia burkei (Tapered Pigtoe), and 25 Hamiota australis (Southern Sandshell). Results of chi-square tests showed significant differences in use of instream habitat types among species (P < 0.05). At all 3 sites, the threatened species were almost exclusively associated with either woody debris or logs. When we found the mussels with leaf pack, we also recorded a majority of the individuals with at least one additional instream habitat (usually woody debris). In contrast, we observed the majority of the common species, E. pullata, either exclusively with leaf pack or, at 1 site, equally with leaf pack and woody debris. Our results suggested that instream habitats associated with threatened mussel species were relatively different from those of the common species.