To develop a simple and reliable method to identify sweetpotato cultivars, we designed cleaved amplified polymorphic sequence (CAPS)-based markers and used them to perform genotyping of Japanese sweetpotato cultivars. In order to screen the CAPS-based markers, 13 primer pairs were designed from the exon sequences of 11 sweetpotato genes to amplify fragments containing an intron. By digesting the amplified products with 8 restriction enzymes having different recognition sites, a total of 27 polymorphic marker fragments were obtained. Genotyping of 60 Japanese sweetpotato cultivars using these markers suggested that the markers can effectively distinguish sweetpotato cultivars. Among the genes used for primer design, the gene encoding the dihydroflavonol 4-reductase (DFR) showed the largest degree of polymorphism. To our knowledge, this is the first report on the development of CAPS-based markers in sweetpotato.