A 'Kyucho' (an intrusion of warm surface water) occurs in the Bungo Channel, located in southwestern Japan. The abundances of Prochlorococcus and Synechococcus during a Kyucho, together with physical and chemical environmental factors, were investigated from the Kuroshio region to the Seto Inland Sea, via Bungo Channel, from 26 November to 5 December 2003. With the occurrence of the Kyucho, oceanic water intruded from the Kuroshio region into the middle of the Bungo Channel. The abundance of Prochlorococcus was the highest in the Kuroshio region and the southern part of the Bungo Channel (> 25 x 10(3) cells ml(-1)), low in the northern part of the Bungo Channel (< 1 x 10(3) cells ml(-1)), and below detection levels in the Seto Inland Sea. A relatively high abundance of Synechococcus cells (> 15 x 10(3) cells ml(-1)) was detected in the Kuroshio region and in the southern part of the Bungo Channel, but the abundance (< 6 x 10(3) cells ml(-1)) was low in other regions. In the Kuroshio region and the southern part of the Bungo Channel, high-phycourobilin (PUB)-type cells were dominant (> 90%); at this location, most of the available light in the deeper layer (> 25 m depth) was in the 450 to 500 nm range, corresponding to the peak absorbance of PUB. In contrast, the abundance of low-PUB-type cells accounted for > 75% of the total in the northern part of the Bungo Channel and in the Seto Inland Sea, where most of the available light in the deeper layer (> 10 m depth) was in the 480 to 560 nm range, including the peak absorbance of both PUB and phycoerythrobilin (PEB). These results indicate that Synechococcus cells of high-PUB type, which have a higher Ex 495:545 (> 1.5; ratio of orange fluorescence intensity excited at 495 nm to that at 545 nm), as well as Prochlorococcus cells were advected to the Bungo Channel by the Kyucho. The co-occurrence of the 2 pigment types of Synechococcus in coastal waters is highly affected by a physical process, such as the Kyucho.