[Objective] We studied the correlation between low nucleic acid content (LNA) bacteria and their filterability. [Methods] Bacterial community and filterability in three freshwater environments were analyzed by flow cytometry (FCM), denaturing gradient gel electrophoresis (DGGE) and statistical analysis. [Results] The proportion of LNA bacteria and their filterability had a significant correlation (y=0.646x+22.42, R2=0.984, P<0.01), and the filterability of LNA bacteria depended on not only the cell size, but also shape and flexibility. In addition, bacteria community organization positively correlated to the proportion of high nucleic acid content (HNA) bacteria and negative correlated to the proportion of LNA bacteria. [Conclusion] The results indicated that 0.45 μm pore-size-filtration can efficiently screen LNA bacteria from the autochthonous microbial community, and demonstrated that bacterial community organization was closely related to the nucleic acid content measured by flow cytometry.