Organic aggregates (OA) in aquatic ecosystems harbour diverse microbial communities. The colonization and growth of OA-attached bacteria are important processes in the degradation and transformation of the particles. The development of efficient and comparative DNA extraction methods is one of the most critical steps in the study of the composition and diversity of OA-attached bacterial communities. To evaluate whether different DNA extraction procedures affect the measurement of bacterial community composition, we compared four in situ lysis procedures using OA from three locations in a shallow eutrophic lake (Lake Taihu, China). The extracted DNA was analyzed using denaturing gradient gel electrophoresis profiles. We found that the choice of DNA extraction protocol had a significant influence on the fingerprints of the OA-attached bacterial community. This was shown not only in the number of bands but also in their relative representation of certain DNA bands. Using the bead-beating DNA extraction method in the presence of hexadecyltrimethylammonium bromide, we found that crude microbial DNA could be extracted efficiently from different OA types. This protocol is reproducible and gives very pure DNA of relatively high molecular mass. More importantly, the protocol provided more representative and informative data on the diversity of OA-attached bacterial communities.