The genus Silene presents significant taxonomic challenges, particularly for groups such as S. sect. Odontopetalae and the monotypic S. sect. Sordidae. This study investigates the evolutionary relationship between the narrowly endemic Silene sordida and the widespread S. odontopetala to resolve these ambiguities. Using a multispecies coalescent framework with five genetic markers and expanded taxon sampling, the species tree and divergence times were estimated. The results revealed a moderately supported sister relationship between S. sordida and S. sect. Odontopetalae, with their divergence estimated at approximately 5.5 million years ago, following the Messinian salinity crisis. Despite their profound morphological and ecological differences, the results suggest a shared evolutionary origin. This study underscores the limitations of morphology-based classification in Silene and highlights the critical roles of ecological divergence, historical biogeography, and convergent evolution in shaping the genus’s diversity. The results provide a clearer understanding of the evolutionary processes driving diversification in these complex lineages.