Myosmine can not be separated from nornicotine, nicotine and anabasine intactly by capillary zone electrophoresis (CZE) with a phosphate buffer. Using citrate solution at pH 6.5 as a CZE buffer, myosmine is protonated intactly by H⁺, charged positively and then separated from other tobacco alkaloids on the baseline. Its sensitivity is ten times higher than gas chromatography (GC) with a nitrogen–phosphorus detector (NPD). The mechanism for protonating myosmine intactly is discussed and the utility of the new method is testified, too.