Vegetational and substrate features for vascular plants in the gravelly floodplains of the middle reaches of the Kinu River in Kanto Region were studied with the special interest in the present status of the threatened river-endemics and biological invasions by alien plants. Hierarchical clustering analysis of the presence / absence data of 550-1452 quadrats (0.5 m × 0.5 m) for each of seven study sites along the middle reaches revealed two site groups characterized by the occurrence of distinct species. The river endemics, Anaphalis margaritacea subsp. Yedoensis, Artemisia capillaris, and Aster kantoensis predominated the vegetation of the ‘upper’ five sites located in the upper part of the middle reaches, but were almost totally absent from the two ‘lower’ sites in the lower middle reaches. The importance index of the river endemics in the sites was negatively correlated with that of alien species represented by Solidago altissima. The current flooding frequency or substrate could not explain the vegetational difference appreciated between upper and lower site groups. In the ‘upper sites’, an alien, Eragrostis curvula, occurred on the channel shelf together with three river endemics, but hardly coexisted with them within the same quadrat. © 2001, Ecology and Civil Engineering Society. All rights reserved.