The genus Apocynum contains perennial bast fiber plants that are spread worldwide. Apocynum species have great application prospect in salt-alkali regions, are rich in flavonoids, and possess medicinal significance. Here, we report the draft genomes of two species, Apocynum venetum and Apocynum hendersonii, and elucidate their evolutionary relationship. The high synteny and collinearity between A. venetum and A. hendersonii suggested that the two species experienced the same WDG event, indicating that divergence might be more recent. Comparative analysis revealed that ApF3H and differentially evolved ApUFGT genes are critical for determining natural variation in flavonoid biosynthesis between relatives. ApF3H-1 enhanced the total flavonoid content and promoted the antioxidant capacity of transformed plants compared to the wild-type plant. ApUFGT5 and 6 explained the diversification of flavonoids or their derivatives. These data provide biochemical insight and knowledge on the genetic regulation of flavonoid biosynthesis, supporting the adoption of these genes in breeding programs aimed at the multipurpose use of plants.