Due to the diversity on anthocyanin content, the sweetpotato germplasm served as natural raw material and offered obvious advantages in high-quality special varieties breeding. In this study, we analyzed the anthocyanin accumulation of 66 sweetpotato accessions and the nucleotide polymorphisms of anthocyanin synthesis genes using molecular markers such as TRAP. The anthocyanins accumulation in storage roots and leaves was independent and not directly related to those in other tissues. The skin color of storage root and the fibrous root is identical, closely associated to the color of fibrous root primordium. Moreover, the analysis by TRAP molecular markers revealed IbCHS, IbDFR and other genes associated with anthocyanin accumulation, which existed multiple copies in the genome, showed higher polymorphism within this collection. The transcriptional factor IbMYB1-2a/b showed a relevance to the accumulation of anthocyanin in storage roots, but not in other tissues. Notably, IbMYB1-2a/b gene was not existed in all purple-fleshed sweetpotatoes. Thirdly, the CHSRV1/ AN4 primer combination was an ideal TRAP marker, which could clarify these 66 germplasm accessions. In relative to these morphological markers, the molecular markers showed advantage in reflection of the genetic relationship between sweetpotato germplasm resources. Thus, this study provided insights on anthocyanin accumulation and also genetic resources that might be valuable in breeding for vegetables and purple-fleshed sweetpotato varieties.