Epitope vaccine is an important part of vaccine research in the future. However, there is no report about fish epitope vaccine so far. Edwardsiella anguillarum is a new bacterial pathogen and outer membrane protein A (OmpA) of E. anguillarum had been identified as a good antigen. In this study, New Zealand white rabbit and European eels (Anguilla anguilla) were immunized by the recombinant OmpA (rOmpA) after it was expressed and purified. The rabbit serum was collected when the anti-rOmpA serum ELISA titer was 1:40000, then IgG in the rabbit serum was separated by protein-A column affinity chromatography. The theoretical epitopes of the OmpA were analyzed by the ABCpred Prediction Server and 19 B-cell linear epitopes were ascertained, then these epitopes were synthesized and coated on the ELISA plate. Three epitopes were identified by the indirect ELISA using the purified IgG, and 2 epitopes were identified by indirect ELISA when the eel serum was used, then a novel common epitope, VETKRFTLKSDVLFNF (215–230), was found when 19 peptides reacted with rabbit and eel antibodies respectively. The B-cell epitope was identified for the first time using rabbit and fish serum simultaneously, and results of this study will provide reference for fish epitope vaccine design.