Repeated adaptation to similar environments can lead to divergence of phenotypes in different populations. Such evolutionary changes sometimes result in incongruence between morphology and molecular phylogeny, for which careful biological investigation is required. Natural phenotypic variation in rheophytic populations of the Solidago virgaurea L. complex (Asteraceae), which evolved multiple times from ancestral dryland forms in Japan, are here reported. Common garden experiments and population genetic analysis were used to evaluate the extent to which parallelly evolved rheophytes diverged in morphological, phenological and genotypic features to understand their complex evolutionary history. Significant divergence among rheophytic populations was detected in multiple traits, even in leaf morphological traits, which are similarly subjected to purifying selection by water pressure in riparian habitats. Whereas most of the variation were attributed to differences between specific pairs of populations, flowering phenology showed latitudinal variation, which likely evolved along a large-scale environmental cline. Multivariate analysis revealed that at least the population on Okinawa Isl., at the edge of the range of the species, is phenotypically distinguishable from rheophytic populations on the main islands. Phylogenetic analysis also suggested that the Okinawan rheophytes are genetically isolated from parapatric dryland populations. Based on the evidence, the Okinawan rheophytic plants are recognized as specifically distinct and are described as Solidago yambaruensis S. Sakaguchi & Mot. Ito.