Peanut (Arachis hypogae L.) is considered one of the main foods and oil crops in Vietnam. The improvement of local Sen peanut varieties is still limited because the identification of the varieties is mainly based on morphological characteristics. In order to identify genomic features and conserve the genetic resources of this variety in Nam Dinh province, an analysis of the genetic diversity of 20 Sen peanut variety samples was conducted using 32 SSR markers. These markers were selected based on their association with important traits of peanuts. The marker TC9H09 is effective for selecting lines with high resistance to rust disease, as indicated by a DNA band size of 220 bp. The markers TC3A12 and TC3E02, with DNA band sizes of 220 bp and 250 bp, respectively, were found to be effective in selecting lines with high oil content. Meanwhile, the marker TC9F10 could be used to select lines tolerant to rust disease and late leaf spot disease, with resulting DNA band sizes of 170 bp, 240 bp, 290 bp, and 350 bp. There were four line groups with high genetic similarity, namely (1,2); (3, 4, 5, 6, 7, 8, 9, 10); (11, 12, 15, 16, 18); and (13, 14, 17, 19, 20). Combining data from phenotypic and genotypic evaluation, it was found that lines 3, 4, 5, 6, 7, 8, 9, and 10 exhibited high resistance to rust disease and had genetic similarity. Similarly, lines 13, 14, 16, and 17 demonstrated high lipid content. These lines, which possess valuable traits for quality and productivity, will be multiplied to effectively improve the genetic resources of the Sen peanut variety in Nam Dinh province.