Global warming is assumed to alter the trophic interactions and carbon flow patterns of aquatic food webs. The impact of temperature on phyto-bacterioplankton coupling and bacterial community composition (BCC) was the focus of the present study, in which an indoor mesocosm experiment with natural plankton communities from the western Baltic Sea was conducted. A 6°C increase in water temperature resulted, as predicted, in tighter coupling between the diatom-dominated phytoplankton and heterotrophic bacteria, accompanied by a strong increase in carbon flow into bacterioplankton during the phytoplankton bloom phase. Suppressed bacterial development at cold in situ temperatures probably reflected lowered bacterial production and grazing by protists, as the latter were less affected by low temperatures. BCC was strongly influenced by the phytoplankton bloom stage and to a lesser extent by temperature. Under both temperature regimes, Gammaproteobacteria clearly dominated during the phytoplankton peak, with Glaciecola sp. as the single most abundant taxon. However, warming induced the appearance of additional bacterial taxa belonging to Betaproteobacteria and Bacteroidetes. Our results show that warming during an early phytoplankton bloom causes a shift towards a more heterotrophic system, with the appearance of new bacterial taxa suggesting a potential for utilization of a broader substrate spectrum.