We studied the community structure and diversity of epiphytic bryophytes in a vertical gradient from tree base to canopy in four lowland rain forest sites of the Colombian Amazon (Amazonas, Caquetá, Putumayo, and Vaupés). Each of the 64 sampled phorophytes was divided into six height zones from the base (Z1) to the outer canopy (Z6). As a subproject, we carried out a genetic population study using the liverwort Cheilolejeunea rigidula (Lejeuneaceae) as our model species, which occurred in all six height zones. In addition to 65 successfully sequenced samples from the study sites, we included individuals of C. rigidula from Guiana and Brazil (Manaus and Tapajos) to investigate the connectivity and genetic structure of this species across the Amazon region and to evaluate the genetic structure based on phorophyte height zones. Each site in Colombia, Brazil and Guiana was considered a subpopulation. The sequenced chloroplast markers (partial atpB gene, partial psbA gene/psbA-trnH spacer) showed little variation across the Amazon and the height zones on the trees. The nuclear marker (ITS) showed a spatial structure indicating genetic differentiation of subpopulations across the Amazon, but little genetic differentiation of C. rigidula along the height of the trees. The gradient across the Amazon shows a relationship between genetic distance and geographic distance, indicating dispersal limitations (P<0.001). At local and regional scales, our results suggest that dispersal can have a dominant effect on populations and communities, increasing connectivity.