The main goal of this study is to predict common and exclusive linear epitopes from two different grouper iridovirus protein sequences and launch their applications to vaccine design. The prediction mechanism is essentially based on integrating previously developed linear/conformational epitope prediction systems, the structural prediction system (Phyre2), and the sequencestructure alignment tools. The predicted two protein structures of iridovirus were aligned by a structure alignment system for identifying virtual structural variations. If the predicted linear epitopes appeared to be the variant geometrical conformations and located on protein surface, they could be assumed as exclusive epitope candidates. Inversely, the conserved linear epitopes located on surface with high antigenicity could be considered as common linear epitopes for vaccine design. Through combining both sequence and structural alignment results and surface structure validation, two conserved segments and one partial conserved segment were found suitable for designing as linear epitopes for the two different iridoviruses. In addition, both grouper iridovirus sequences possess one unique segment respectively, and which can be considered as exclusive liner epitope for each iridovirus. All these predicted linear epitopes would be evaluated by suitable biological experiments for further verification.