We first surveyed the DNA polymerase (pol) gene of cyanopodoviruses and the 16S-23S rRNA gene internal transcribed spacer (ITS) region of picocyanobacteria in a paddy field of northeast China. A total of 49 DNA pol clones and 76 ITS clones were obtained. The blast search results showed that all DNA pol clones and nearly 50% of the ITS clones had up to 76% and 50% identity/similarity to known sequences, respectively. Phylogenetic analyses showed that the DNA pol clones were narrowly distributed in the phylogenetic tree, and two new subclusters of cyanopodoviruses (PG-Pol-I and PG-Pol-II) specific to paddy field were discovered. In contrast, the distribution of ITS clones was very broad, and seven paddy-specific groups of picocyanobacteria (PG-Picocya-I-VII) were identified. In general, novel groups of cyanopodoviruses and picocyanobacteria were observed in this study, suggesting that coevolution between cyanopodoviruses and their hosts occurs in the paddy field.