A new cyanophage, strain S-KM1, infecting a phycoerythrin-rich Synechococcus sp., strain KFM001, was isolated from seawater of Kagoshima Bay. Transmission electron micrography of negative-stained specimens revealed that the phage isolate has an isometric head with a diameter of 83 nm and a contractile tail 166 nm in length and that it belongs to the family Cyanomyoviridae. The cyanophage was apparently virulent to the host strain KFM001 with a burst size of less than 70-80. The cyanophage may affect the population structure of the dominant picoplankton species in Kagoshima Bay.