To analyze the quaternary ammonium compound, benzalkonium chloride (bak) a biocide uses in molasses, by using ion suppression chromatography. The analytical condition consists of acetonitrile : phosphate buffer (50:50 v/v) as mobile phase, adjusted pH to 5.00+-0.01, hypurity cyano column (4.6 mmi.d x 250 mm), flow rate 1.00 ml/min. The bak was detect by uv-vissible photodiode array detector at wavelength 210 nm. This method can detect homologue C12 and homologue C14. Another method used to analyze bak was ion pair chromatography which the analytical procedure composed of methanol:5 mM heptane sulfonic acid sodium salt (50:50 v/v) as mobile phase, adjusted pH to 3.50, flow rate 1.00 ml/min, Novapak C18 column (3.9 mmi.d x 150 mm) and the amount of bak could be detected. However, this method could not detect the homologue C12 and C14. Due to the color of the molasses interfere with the analysis, thus solid phase extraction was use to eliminate the color of samples. The sep pak ODS was not able to get rid of color in molasses, while the used of sep pak extract-clean cyano and acetonitrile: phosphate buffer (70:30 v/v) adjusted pH to 5.00+-0.01 as eluent could get rid of the color interference. From this condition when detect by ion suppression, the color in molasses disappeared and the result showed that both homologue C12 and homologue C14 of bak were detected in only 3 samples out of 13. The amount of homologues C12 and homologues C14 were detected in the order of 5%>7%>15%.