Differences between individuals collected from sun and shade populations could result from either somatic or genetic differences, particularly in populations of perennial plants. Our objective in this study was to separate somatic from genetic differences. We collected Anthoxanthum odoratum and Plantago lanceolata from sun and shade populations and made measurements on both vegetatively propagated clones and seed progeny from each clone. The parental populations differed in a wide range of physiological and morphological traits. However, only photosynthetic capacity was significantly different between both the original sun and shade populations and their seed progeny. In both species, plants from the sun population had higher photosynthetic capacities than those from the shade population when grown in a common environment. This demonstrates that there was genetic differentiation between the sun and shade populations. Photosynthetic capacity of parents and offspring also differed, suggesting a somatic effect. Since many of the original clones were virus-infected, but all but one of the offspring were virus-free, this might have been a result of virus infection. However, in spite of the fact that the parents and offspring clones were propagated vegetatively so that the plants were at the same developmental stage at the time of measurement, we cannot rule out the possibility that differences in age of cell lines could also have been a factor.