Molecular phylogenetic analysis was conducted using single-nucleotide polymorphism data from Chinese plants with pubescent stems, similar to Cassytha filiformis var. duripraticola, which has been known to distribute in Japan and Taiwan. The phylogenetic analysis demonstrated that the Chinese plants were included in the same clade with plants of C. filiformis var. duripraticola obtained from Japan and Taiwan. This study is the first report of C. filiformis var. duripraticola from Mainland China based on the morphological and molecular features.