The consequences of ocean acidification for heterotrophic marine bacteria remain under debate and almost nothing is known concerning marine fungi. Previous studies were carried out in large-scale mesocosms, where indirect effects mediated through complex food web interactions come into play. Here we present an alternative approach, using highly replicated microcosms (1-1.6 L). Focusing on bacteria and fungi, we wanted to investigate whether direct pH effects on community structure and abundances occur. Additionally we aimed to identify the groups reacting to pH reductions. We incubated the natural microbial community from Helgoland Roads (North Sea) for four weeks at in situ seawater pH, pH 7.82 and pH 7.67. To reveal changes in community structure, we applied the fingerprint method Automated Ribosomal Intergenic Spacer Analysis (ARISA). Bacterial communities were furthermore analyzed by 16S ribosomal amplicon pyrosequencing. Abundances were determined by flow cytometry (bacteria) and colony forming unit counts (fungi). We repeated the experiments in different seasons and years and applied different dilution culture strategies to look at diversely assembled communities. We predominantly found pH-dependent shifts in community structure at pH 7.82 for bacteria and at pH 7.67 for fungi. Bacterial abundance was not influenced by pH, while fungal numbers were on average 9 times higher at pH 7.82 and 34 times higher at pH 7.67. Different members of Gammaproteobacteria, Flavobacteriaceae, Rhodobacteraceae and Campylobacteraceae reacted to pH reductions. While Rhodobacteraceae were less characteristic for reduced pH, Pseudoalteromonadaceae and Campylobacteraceae profited from pH reductions. For most other bacterial groups, we did not observe consistent trends in the direction of the pH response. Our findings demonstrate that already small reductions in pH have direct effects on bacterial and fungal communities. Although total bacterial abundance was not affected, both naturally abundant and rare bacterial groups reacted to pH reductions. The strong increase in fungal numbers at reduced pH suggests that fungi may reach higher importance in marine biogeochemical cycles and as infectious agents with ocean acidification. A 454 pyrosequencing approach is currently planned to resolve fungal identities.