We studied the effects of virus infection on dynamics of three Eupatorium makinoi populations in contrasting light environments, Gora-dani (a shaded population) and Minou 1 and Minou 2 (open-site populations). Censuses of the plants were taken for 8 yr in Gora-dani and 4 yr in Minou 1 and Minou 2. After the epidemics of virus infection, most plants were virus infected at both sites. The number of plants and the proportion of flowering individuals decreased rapidly and simultaneously in the shaded population in Gora-dani. By contrast, in the open-site populations of Minou, the proportion of flowering plants decreased first, and then the number of plants decreased gradually. Growth analysis of the plants in the Gora-dani population revealed that stem growth was significantly suppressed by infection and that flowering and survivorship of the infected plants decreased with reducing plant height. Since light availability affected plant growth and thereby flowering and survivorship, the differences in population dynamics between the two field sites could be caused by the differences in light environments. Although populations in open sites may persist for considerable periods after virus epidemics, the individual local populations of E. makinoi would eventually become extinct irrespective of light environments.