The incidence of freshwater algal bloom has been increasing globally in recent years and poses a major threat to environmental health. Cyanobacteria are the major component of the bloom forming community that must be monitored frequently. Their morphological identities, however, have remained elusive, due to their small size in cells and morphological resemblances among species. We have analyzed molecular diversity and seasonal changes of cyanobacteria in Paldang Reservoir, Korea, using morphological and 16S rRNA pyrosequencing methods. Samples were collected at monthly intervals from the reservoir March-December 2012. In total, 40 phylotypes of cyanobacteria were identified after comparing 49,131 pyrosequence reads. Cyanobacterial genera such as Anabaena, Aphanizomenon, Microcystis and Synechocystis were predominantly present in samples. However, the majority of cyanobacterial sequences (65.9%) identified in this study were of uncultured origins, not detected morphologically. Relative abundance of cyanobacterial sequences was observed as high in August, with no occurrence in March and December. These results suggested that pyrosequencing approach may reveal cyanobacterial diversity undetected morphologically, and may be used as reference for studying and monitoring cyanobacterial communities in aquatic environments.