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• Selenoneine monomer, dimer and ergothioneine were extracted from genetically modified yeast with boiling water. • The compounds were separated by HPLC using a pentabromobenzyl column. • This method purified selenoneine monomer from ergothioneine without reducing agents. Selenoneine is an organic selenium compound found in blood of tuna. Selenoneine has two conformational structures: the reduced monomer, and the oxidized dimer formed through a Se-Se bond. Presence of the two forms depends on the environmental chemical properties and oxidative conditions. The selenoneine dimer has been isolated from a genetically modified fission yeast following fermentation but the selenoneine monomer has not been reported because it co-elutes with ergothioneine due to their chemical similarity between selenium and thiol functional groups. In this study, we investigated the separation of selenoneine monomer and ergothioneine in aqueous solutions by high-performance liquid chromatography using a pentabromobenzyl column characterized by London dispersion force interactions. Selenoneine monomer and ergothioneine were completely separated, with a peak resolution (Rs) of 4.16. The obtained selenoneine had a purity of 88.4% as a selenium compound and the recovery efficiency was 52.8%. This is the first method reported for the separation of selenoneine monomer. [ABSTRACT FROM AUTHOR]