In this study, the physicochemical properties of starches from transgenic sweetpotato plants modified by RNA interference of the starch synthase II (SSII) gene were examined. The method of genetic manipulation developed during our previous study using White Star cultivar was applied to Konahomare cultivar, which has promising features of high yield and high starch content. SSII gene suppression resulted in the following consistent effects being observed in both cultivars: lowering of gelatinization temperature and gelatinization enthalpy, increase in B-type feature in X-ray diffractograms, decrease in the phosphate content of starch and alteration in chain-length distributions as determined by gel-permeation chromatography and high-performance anion-exchange chromatography. Furthermore, starches from all transgenic lines showed slower retrogradation and higher digestibility by glucoamylase compared to those from control starches. These traits of transgenic starches were similar to those from a starch of Quick Sweet cultivar, suggesting that mutation in the SSII gene could be one of the reasons for the unique property of starch in Quick Sweet. Thus, our RNA interference technique for sweetpotato was successfully applied to starch engineering in the promising cultivar of sweetpotato for starch material, Konahomare. The SSII gene inhibition significantly modified the basic architecture of starch and subsequently altered its functional properties.