Fecal pellets make up a significant fraction of the global flux of organic matter in oceans, and the associated bacterial communities in particular are a potential food source for marine organisms. However, these communities remain largely unknown. In the present study, the bacterial communities on fecal pellets of the benthic copepod Paramphiascella fulvofasciata feeding on the diatoms Navicula phyllepta and Seminavis robusta were analyzed. The aim of this study was to characterize the bacterial communities associated with the diatoms and the fecal pellets by means of DGGE profiling. Furthermore, isolated bacteria were characterized by means of partial 16S rRNA gene sequencing. The composition of the bacterial microflora on fecal pellets was studied in terms of the effect of the original food source, the age of the fecal pellets and the copepod's identity. Alphaproteobacteria, Flavobacteria, and Bacilli were found on the fecal pellets; whereas on diatoms, exclusively Gammaproteobacteria were identified. Especially after eating N. phyllepta, there was an important increase in bacterial diversity, although the diatom N. phyllepta harbored a less diverse bacterial community than S. robusta. Our data suggest that the additional bacteria originate from the copepod's digestive tract and largely depends on the initial food source.