In this study, we surveyed cyanopodovirus DNA polymerase (pol) sequences in paddy waters using the culture-independent PCR and Sanger sequencing methods. Four paddy waters generated from a pot experiment with different soil types collected from op E: n paddy fields in northeast China were used in this study. A total of 438 DNA pol clones were identified as cyanopodoviruses. The clones from the paddy waters formed nine unique groups of cyanopodoviruses either exclusively or with clones from East Lake in China (subclusters α-1 to α-8 and cluster β). None of the clones from open oceans or coastal waters fell into these unique groups. Additionally, the distribution proportions of the clones into different cyanopodovirus groups varied among paddy water samples, which suggested that the cyanopodovirus compositions were spatially distributed in the paddy fields. The comparison of clone libraries in different studies indicated that the diversity of cyanopodoviruses in paddy waters was comparable to the diversity in the open oceans but was less than the diversity in the coastal estuary of Chesapeake Bay. Non-metric multidimensional scaling analysis indicated that the cyanopodovirus communities in paddy waters were similar to those in lake freshwater but distinct from the communities in marine and coastal waters.