The influence of habitat connectivity on dispersal limitation and genetic structure in bryophytes is relatively well researched; however, little is known as to how habitat insularity may impact phenotypic divergences on a continental scale. Here we conduct a morphometric analysis of five quantitative gametophytic traits from two Amazonian Calymperaceae (Syrrhopodon helicophyllus and Calymperes lonchophyllum) from contrasting habitats (Amazonian white-sands and terra firme forests) to test whether increased habitat insularity is correlated with greater inter-population divergence in phenotypic variation. We also test how much of the phenotypic variation among the two taxa is explained by three environmental variables (altitude, mean annual temperature and mean annual precipitation). The Amazonian species endemic to continuous terra-firme forest (C. lonchophyllum) revealed greater geographic structure in phenotypic variation that that of its counterpart (S. helicophyllus) of more insular white-sands forest habitats. Furthermore, environmental variables explained more of the phenotypic variation among populations of S. helicophyllus than for those of C. lonchophyllum. We attempt to explain these patterns as a result of either historical factors, divergent adaptive reproductive strategies, phenotypic plasticity and/or differences in the spatial scales of sampling effort among the two species. Understanding the role of habitat heterogeneity on speciation processes is a priority for understanding the origin and maintenance of floristic richness in the Amazon Basin. We propose that bryophyte studies highlighting morphometric data coupled with population genetic structure would greatly contribute to our understanding of evolutionary processes in this megadiverse Biome.