The actiniarian sea anemone, Entacmaea quadricolor, and the scleractinian coral, Alveopora japonica, host symbiotic dinoflagellates belonging to the genus Symbiodinium (Freudenthal). We studied the host-symbiont specificity of these two anthozoan hosts in the northwestern Pacific Ocean. Symbionts within the two hosts were identified using partial large subunit (LSU) ribosomal DNA (rDNA) and complete internal transcribed spacers (ITS) 1 rDNA regions. The host, E. quadricolor, was identified using the partial LSU rDNA molecular marker. Genetic analysis showed that E. quadricolor only harbors dinoflagellates belonging to subclade C1/3 of the genus Symbiodinium. Moreover, no genetic variation was detected among the symbionts of E. quadricolor within the study region (Korea and Japan), even though the two distant sites were separated by more than 1000 km, at collection depths of 1 m in shallow and 13-16 m in deep water. Whilst scleractinian corals host multiple Symbiodinium clades in tropical waters, A. japonica, sampled over a wide geographical range (800 km) within the study region, only hosts Symbiodinium sp. clade F3. The high specificity of endosymbionts in E. quadricolor and A. japonica within the northwestern Pacific Ocean could be accounted for because symbiotic dinoflagellates within the host anemones appear to be acquired maternally, and the Kuroshio Current might affect the marine biota of the northwestern Pacific. However, the consistency of the symbiotic relationships between these two anthozoan hosts and their endosymbionts could change after climate change, so this symbiotic specificity should be monitored.