Scirpus L. s.l. is well known as one of the polyphyletic groups in Cyperaceae. Recent molecular phylogenetic studies clearly suggested that Scirpus s.l. should be separated into several independent genera. In this study, we intend to present the morphological variations and patterns of phenotypic evolution based on molecular phylogeny of Korean Scirpus s.l. Five genera, including 21 taxa from Korean Scirpus s.l., were examined: three species of Bolboschoenus, three species of Schoenoplectus, eight species of Schoenoplectiella including one hybrid, five species of Scirpus, and two species of Trichophorum. For morphological analyses, 23 and 48 characters were selected from vegetative and reproductive organs, respectively. Molecular phylogeny was inferred from a nuclear ribosomal internal transcribed spacer, the chloroplast rbcL gene, and the chloroplast trnL-F region. Distinct characteristics and quantitative variation was presented for identification of the five genera and their species. A pronounced pattern of morphological character change was reduction, although many other character states seem to be homoplastic. We suggest that the reduction of phenotypic characteristics has been expressed in terms of condensation of internodes, reduction of leaf blade, and simplification of inflorescence among five genera of Korean Scirpus s.l.