In February 2005, a mass mortality of giant abalone Haliotis (Nordotis) gigantea Gmelin, 1791 occurred on a private abalone farm in Shimane Prefecture, Japan. The cumulative mortality rate reached about 84%. In histological observations, bacteria-like spherical particles were found in affected animals, suggesting a bacterial infection. Many of the bacteria-like particles were found in the cells that were presumably host phagocytes. DNA was extracted from the hemolymph of a diseased abalone and a bacterial 16S rRNA gene was amplified by PCR. The bacterium was classified within the genus Francisella by gene sequence analysis. A bacterial isolate was obtained by spreading hemolymph of a diseased abalone on modified Eugon agar dissolved in 70% seawater containing 1% (w/v) hemoglobin. A gene fragment of the expected size was amplified from the bacterial isolate by PCR using specific primers for the 16S rRNA gene obtained from the diseased abalone. Experimental infections were carried out by intramuscular injection with the bacterial isolate or by immersion in the bacterial suspension using 2 species of abalone, the giant abalone and the Japanese black abalone Haliotis (Nordotis) discus discus Reeve, 1846. Most (98.6%) of the abalone challenged with the bacterial isolate died in experimental infections. These results suggest that the Francisella sp. isolate was the causative agent for the mass mortality of giant abalone. This is the first report of a pathogenic Francisella sp. isolate for mollusks.