Abstract: As one of the key agronomic traits that determine ornamental value, the genetic mechanism of flower color in lotus (Nelumbo nucifera Gaertner) requires further exploration. In this study, an F₂ segregating population was obtained with the lotus cultivar ‘Mantianxing’ (red flower) as the female parent and ‘Juwuba’ (white flower) as the male parent. A high-density genetic map of the lotus was constructed using specific locus amplified fragment sequencing (SLAF-Seq). Combined with the phenotypic information of the F₂ individuals obtained over two consecutive years, QTL mapping of the flower color trait was carried out. PARMS molecular markers linked to this trait were also developed. The integrated map spanned a genetic distance of 1046.82 cM, which consisted of 6376 SLAF markers on eight linkage groups, with an average genetic distance of 0.16 cM between adjacent markers. A QTL potentially responsible for red and white flower colors was stably detected on the sixth linkage group, with a contribution rate of 49.957%. Eighteen genes were located in the QTL interval, five of which were identified as candidate genes associated with flower color. Three PARMS markers were developed that could be effectively used for genotyping red and white flowers in F₂ individuals.