Respiration in marine bacteria (fraction <0.6 µm) was investigated in 5 distinct coastal ecosystems. Respiration rates were estimated from the decrease of dissolved oxygen (O2) concentrations measured with a fibre-optic oxygen sensor (optode) during short-term incubations (5 to 6 hours) in the dark. Sub-populations of heterotrophic bacteria were defined and enumerated by flow cytometric analysis. Respiration rates ranged from 0.04 to 0.14 µmol O2 l−1 h−1 and were not correlated to total bacteria abundances. In contrast, they significantly increased with the relative proportion of HDNA cells (i.e. high deoxyribonucleic acid content) within the bacterioplankton community. These results stress the need to relate bacterial respiration rates to the absolute and relative abundance of the different cytometrically defined sub-populations found in bacterial assemblages, rather than to total cell counts. This result indicates that only a fraction of bacterial cells may contribute to bacterial respiration, which indicates a reconsideration of the relevance of some previous estimates of bulk bacterial respiration and the related biogeochemical fluxes may be required.