Haw pectin obtained by cold-water extraction displayed higher viscosity than that of commercially available lemon pectin. After hydrolysis using purified polygalacturonase, haw and lemon pectins yielded polygalacturonase-resistant fractions (CP1-1 and LP1-1, respectively) in the high-molecular-weight region. Anion-exchange chromatography of the resistant fractions yielded additional three fractions (Hf1, Hf2, Hf3) for CP1-1 and 2 fractions (Lf1, Lf3) for LP1-1. The acidic fractions Hf3 and Lf3 were similar in structure; however, the sugar content of the neutral fractions Hf1 and Lf1 differed. The structural differences in the fractions Hf1 and Lf1, and the presence or absence of the acidic fraction Hf2 in the pectin molecule might be associated with the difference in viscosity between haw and lemon pectins. Structural analysis revealed that fraction Hf2 was a polysaccharide in which approximately one-third of the main chain was composed of alpha-1,4-linked GalA, and no alpha-1,4-linked GalA was present in the remaining two-thirds pectolyase-resistant region. Furthermore, the constituent sugars Gal and Man existed quantitatively in the pectolyase sensitive region of Hf2.