Objective:To understand the molecular evolutionary and genetic differences of South-East Asian dodeca RNA viruses (Seadornavirus).Methods:The homology, phylogeny, physicochemical properties, epitope prediction, tertiary structure and surface charge distribution were analyzed based on genome sequence of Seadornavirus capsid proteins.Results:The time of most recent common ancestor (tMRCA) of Seadornavirus was estimated to be about 2 359 years ago, which were divided into three clusters. Their tMRCA were about 1 338, 499 and 253 years ago, respectively. And their mean substitution rate of Seadornavirus was 3.6×10 -4 n/s/y. The homology of nucleotide and amino acid was 31.3%-100% (μ=68.0%) and 11.9%-100% (μ=56.0%) respectively. Physicochemical properties and epitope analysis showed that the Banna virus (BAV) capsid protein is an acidic hydrophobic protein that there are 6 B cell epitopes and 2 Th epitopes, while Liaoning virus (LNV) and Kadipiro virus (KDV) are alkaline hydrophilic protein that there are 3 and 5 B cell epitopes, respectively. And there is only 1 Th epitope in the capsid protein of LNV, while KDV does not contain this epitope. The tertiary structure and protein surface charge analysis showed that the alpha helices and beta folds of Seadornavirus were different and the BAV contains two distinctly positively charged regions and two negatively charged regions, LNV has only one positively charged region, and KDV has two positively charged regions. Conclusions:Seadornaviruses had more rapid evolution and strong adaptability, and the genome sequences, protein epitopes, physicochemical properties and the tertiary structures between Seadornaviruses are different.