The abundance of thraustochytrids was investigated in and off the Seto Inland Sea, Japan. Thraustochytrid cells were stained with acriflavine and counted directly by epifluorescence microscopy. Thraustochytrids were present in the water column at a density of 2.1 x 10(3) to 5.6 x 10(4) cells l(-1), with an overall average of 1.0 x 10(4) cells l(-1), which was about 10(-5) to 10(-6) of the bacterioplankton abundance. In contrast to the low abundance of thraustochytrids, their biovolume was estimated to compose a not negligible fraction of marine microbiota, corresponding to about 3 to 43% of the bacterioplankton biovolume. Thus, it is suggested that thraustochytrids play an ecological role as alternative food sources for picoplankton feeders, as well as being active degraders and consumers in aquatic microbial food chains.