The distribution of the main microbial loop components (bacteria, heterotrophic nanoflagellates (HNF), ciliates) was investigated at three sites: the inner, central and outer regions of Hiroshima Bay, Seto Inland Sea, Japan, in summer (June and August 1996 and July 1997). At the inner region site, lower salinity and higher concentrations of nutrients and chlorophyll a were observed than in the other regions. Bacterial, HNF and ciliate biomasses ranging from 32.6 to 170.1 µg C/L, from 1.5 to 84.8 µg C/L and from 0.1 to 91.7 µg C/L, respectively, were generally highest at the inner region site. The ciliate assemblages were mostly dominated by mixotrophic aloricate ciliates in the surface and near-surface layers. The relationship between the biomass of aloricate ciliates and their prey organisms showed significant linear correlations at the three sites. The slope of the regression line was lowest and the X -axis intercept of the line was highest at the inner region site, possibly suggesting relatively low energy transfer efficiency between them in this site. Hence, high biomass of less than 20 µm phytoplankton, bacteria and HNF may not be efficiently utilized by ciliates in the inner region of Hiroshima Bay, compared with the situation in other regions of the bay. [ABSTRACT FROM AUTHOR]