Abstract: The selection of chromatographic optimization criterion is evaluated. Using natural logarithm of the ratio of retention volume of component (i) to reference component (s) in the chromatogram as a function of the retention behavior of each component, the differences between the In (V_R(i))/V_R(s)) of adjacent pairs of substances were proposed as a measure of separation selectivity. Conditions of reversed phase chromatography of 15 naturally occurring protoberberine type quaternary alkaloids were optimized. On Nucleosil 5 C₁₈ column (25 cm×4 mm) at 45℃ with detection at 346nm, isocratic elution with CH₃CN-H₂O (30:70) containing 20 mmol/L KH₂PO₄ at 1.5 ml/min is suitable for the separation of 13 protoberberines. The other two, berberubine and palmatrubine, must be eluted with a mobile phase whose pH value is tess than 3.5. Analysis of the data obtained showed the relations between the different functional groups at different positions on protoberberine ring system and the retention values in the chromatogram.