Sweetpotato varieties with high carotene content have high value for human health. This work aims to improve the breeding efficiency of special varieties with high carotene content by combining molecular markers and agronomic traits to evaluate and screen the parents. The cluster analysis was carried out to identify and screen promising parents by utilizing phenotypic results of the agronomic and characteristic traits, and RAPD and ISSR markers of 15 parents and their offspring by group crossing. Among different parental materials, greater variations were observed in two important traits, the carotene content and the storage root yield. Negative correlation was found between the carotene content and both fresh and dried root yields. The most significant positive correlation was between the carotene content of parents and that of their offspring, with the coefficient of correlation value of 0.7932**. The relationship based on the agronomic characters of the trial materials was not in agreement with the known genealogy, while that based on the molecular marker data showed better result. Each primer amplified 13.8 bands of ISSR markers on average, in which the rate of polymorphic loci was 89.6%. 9.4 bands of RAPD markers were amplified per primer, in which the rate of polymorphic bands was 74.46%. Large genetic variation of carotene content was found among the parents. For analyzing the genetic diversity of sweetpotato, the molecular marker methods were better than morphological traits; ISSR markers were more efficient than RAPD markers. The combination of molecular markers and agronomic trait analysis may provide valuable theoretic basis for selection of parents to breed new varieties with high carotene content.