In general, even within a local area, many common plant species are found in different types of environment. We propose that if the association of a common plant species with different types of environment is investigated, by analysing all individuals in a given population as a single entity, the results might be misleading or incomplete owing to intraspecific variation. To test this hypothesis, we used molecular markers to classify mature Castanopsis chinensis individuals with a diameter at breast height ≥ 40 cm into different genetic groups and analysed the associations of these groups with topographic features and habitats within a 20-ha Dinghushan forest plot, South China. Our results indicated that the different groups had different topographical associations, and that the spatial distributions and genetic structures of individuals varied among the groups. Therefore, if significant genetic structure exists in the population of a common species within a community, to understand the relationship between the spatial distributions of individuals in the population and the environment, it is necessary to classify the individuals into genetic groups and analyse the data for these groups, rather than for a combined group of all individuals.