Edwardsiella bacteria infect Japanese medaka Oryzias latipes; however, the difference in susceptibility between E. piscicida and E. anguillarum is unknown. ​In this study, we performed challenge tests with medaka using four Edwardsiella strains, which were difficult to be identified by specific primers. ​The four strains were reclassified as three E. piscicida strains and one E. anguillarum strain using phylogenetic analysis. ​The immersion challenge demonstrated that medaka were more susceptible to E. piscicida than to E. anguillarum. ​Increases in the bacterial copy number in the infected medaka kidneys were correlated with the worsening of the external symptoms. ​Medaka is considered a valuable model organism for understanding the etiology of edwardsiellosis.