Orchid seeds are presumably dispersed by wind due to their very small size and thus can potentially travel long distances. However, the few related studies indicate that seeds fall close to their mother plants. Because seed dispersal and colonization patterns can have relevant consequences for long-term species persistence, we assessed the fine-scale genetic structure of the epiphytic orchid Epidendrum rhopalostele to provide insight into these patterns. All individuals in the studied population were georeferenced and genotyped with AFLP-markers. Genetic structure was evaluated at two levels (forest and tree) using three approaches: principal coordinates analysis, model-based clustering, and spatial autocorrelation analysis. Results showed two genetic groups, composed of individuals from almost every tree with orchids. Spatial autocorrelation analysis at the forest level found no significant genetic structure when all individuals were considered, but a pattern of genetic patches was revealed when the analysis was performed separately for each group. Genetic patches had an estimated diameter of 4 m and were composed of individuals from more than one tree. A weak genetic structure was detected at the tree level at distances less than 1.5 m. These results suggest that many seeds fall close to the mother plant and become established in the same host tree. Additionally, a sequential colonization process seems to be the predominant mode of expansion, whereby progeny from orchids in one tree colonize neighboring trees. Thus, the existence of two distinct genetic groups and the presence of genetic patches should be considered when seed sampling for ex situ conservation.