We presented a comprehensive phylogenetic analysis of Parnassia covering approximately 80% of recognized species. By integrating five plastid markers ( rbcL , matK , rpl32 - trnL , trnT - trnL and trnL - trnF ) with nuclear marker ITS sequences and applying both maximum parsimony and Bayesian inference approaches, we reconstructed robust phylogenetic relationships within the genus. We presented notable differences between molecular phylogeny and the established sectional classification. While Parnassia sect. Fimbripetalum emerged as monophyletic with strong support, P. sect. Saxifragastrum , P. sect. Cladoparnassis , P. sect. Nectaroquinquelobos , and P. sect. Allolobos were resolved as paraphyletic. The monotypic P. sect. Nectarobilobos represented a distinct evolutionary lineage, whereas the species-rich P. sect. Nectarotrilobos was dispersed across multiple clades. Notably, three eastern Himalayan species ( P. faberi , P. esquirolii and P. labiata ) formed a well-defined clade with highly reduced staminodia. This study provided a critical molecular framework for reevaluating morphological evolution and revising the infrageneric classification of Parnassia .