Sea anemones and associated crustaceans are important components of coral reefs, but their population structure and microhabitat use remain poorly understood. We quantified both types of patterns for two sea anemone and 10 crustacean species at Akumal Bay, Mexico. Rosetip anemones, Condylactis gigantea (Weinland, 1860), occurred as solitary individuals on patch reefs throughout the midbay, while sun anemones, Stichodactyla helianthus (Ellis, 1768), formed dense aggregations on reef patches in the inner bay. Both populations were abundant with exponential size distributions that indicated potentially high recruitment and stable population structure. Individuals of corkscrew anemones, Bartholomea annulata (Le Sueur, 1817), were too rare to analyze their population structure. Crustaceans significantly segregated their microhabitat use among zones on the anemone bodies. Most exhibited exponential size structure, but the chaotic size patterns of some crustaceans suggested recently-sporadic recruitment. We report a previously undocumented association of blue-legged hermit crabs, Clibanarius tricolor (Gibbes, 1850), and anemones; crabs clustered along the anemone columns, and possessed an external, removable coating that protected them from host toxins. We conclude that some anemones and crustacean associates exhibit strong partitioning of habitat and stable population structure on these coral reefs.