Pectin was enzymatically extracted from industrial lemon pomace by using an endo-polygalacturonase from Aspergillus niger as a processing aid and compared to pectin extraction by hot hydrochloric acid. The yield of pectin was 17.6 and 20.2% with enzymatic and acidic treatments, respectively. The molecular weight distribution did not vary greatly between the samples extracted with enzyme or acid. Large differences in charge density were observed, however, when the samples were analyzed by anionic-exchange chromatography. Pectin extracted by the enzymatic treatment indicated higher charge density than that obtained by hydrochloric acid. The higher charge density could due to the presence of endogenous lemon pectinesterase, which was activated at low pH 4.5 in situ conditions during the process of enzymatic extraction, leading to low methoxylated pectin with a higher charge density.