Five acylated peonidin glycosides were isolated from the pale gray-purple flowers of a duskish mutant in the Japanese morning glory (Ipomoea nil or Pharbitis nil) as major pigments, along with a known anthocyanin, Heavenly Blue Anthocyanin (HBA). Three of these were based on peonidin 3-sophoroside and two on peonidin 3-sophoroside-5-glucoside as their deacylanthocyanins; both deacylanthocyanins were acylated with caffeic acid and/or glucosylcaffeic acids. By spectroscopic and chemical methods, the structures of the former three pigments were determined to be 3-O-[2-O-(6-O-(trans-caffeoyl)-beta-D-glucopyranosyl)-beta-D-glucopyranoside], 3-O-[2-O-(6-O-(3-O-(beta-D-glucopyranosyl)-trans-caffeoyl)-beta-D-glucopyranosyl)-6-O-(4-O-(6-O-(3-O-(beta-D-glucopyranosyl)-trans-caffeoyl)-beta-D-glucopyranosyl)-trans-caffeoyl)-beta-glucopyranoside], and 3-O-[2-O-(6-O-(trans-caffeoyl)-beta-D-glucopyranosyl)-6-O-(4-O-(6-O-(3-O-(beta-D-glucopyranosyl)-trans-caffeoyl)-beta-D-glucopyranosyl)-trans-caffeoyl)-beta-D-glucopyranoside] of peonidin. The structures of the latter two pigments were also confirmed as 3-O-[2-O-(6-O-(trans-caffeoyl)-beta-D-glucopyranosyl)-beta-D-glucopyranoside]-5-O-beta-D-glucopyranoside, and 3-O-[2-O-(6-O-(trans-caffeoyl)-beta-D-glucopyranosyl)-6-O-(4-O-(6-O-(3-O-(beta-D-glucopyranosyl)-trans-caffeoyl)-beta-D-glucopyranosyl)-trans-caffeoyl)-beta-D-glucopyranoside]-5-O-beta-D-glucopyranoside of peonidin. The mutation affecting glycosylation and acylation in anthocyanin biosynthesis of Japanese morning glory was discussed.