A factorial design was used to assess the roles of turbulence and viral infection in prokaryotic production and diversity in a spring phytoplankton bloom experiment in the Bay of Ville-franche, France, Several consistent trends were observed in 2 experiments: (1) turbulence stimulated prokaryotic production, (2) prokaryotic cell length increased in experimental turbulence and virus treatments, and (3) organic micro-aggregates with attached prokaryotes formed only in the turbulence treatments and seemed to be reduced in the presence of viruses. We conclude that turbulence likely influenced prokaryotes indirectly by affecting micro-aggregate formation and nutrient availability, Turbulence and viruses had only small influences on the number of bacterial and archaeal bands detected by 16S rRNA gene denaturing gradient gel electrophoresis. However, taking into account presence versus absence of specific bands and their intensities, we detected strong effects in the experiments. We not only detected a negative effect of viruses, but also found that some bands increased in intensity in the presence of active viruses, e.g. one of 3 phylotypes affiliated with the Rhodobacteriaceae. In both experiments, several consistent patterns were found: (1) a phylotype affiliated with Roseobacter was negatively affected (in terms of band intensity) by viruses and turbulence, (2) the relative band intensity of a Rhodobacter increased in the turbulence treatments, and (3) a phylotype related to Oceanospirillum was detected only in the turbulence treatment. We suggest that turbulence and viruses play a significant and previously neglected role in shaping prokaryotic diversity, aggregation and production.