The estuarine copepod Acartia tonsa naturally carried diverse strains of bacteria on its body. The bacterial community composition (BCC) remained very conservative even when the copepod was fed different axenic algal species, indicating that the food per se did not much affect BCC associated with the copepod. In xenic algal treatments, however, copepod-associated BCC differed with each alga fed, even though the same bacterial source was used to inoculate the algae. In addition, starved copepods taken at the same location but at different times significantly differed in their BCC. Algal species composition and copepod life history therefore serve to regulate BCC associated with copepods, and spatial and temporal variations in algal species composition and copepod origin would alter bacteria-copepod interactions.