Patch size and connectivity are the main predictors of population demographic and genetic stability. Habitat fragmentation continues at unprecedented rates justly affecting plant functional connectivity worldwide. However, few terrestrial plant groups have sufficiently foreshortened generation times in which to empirically disentangle the demographic and genetic consequences of reduced patch size and connectivity. Herein, we combine evidence from long-term (15 yr.) population censuses of two epiphyllous bryophytes and population genetic estimates in an experimentally fragmented Amazonian landscape to create a profile of the eco-evolutionary impacts of reduced habitat connectivity. Single nucleotide polymorphisms (SNPs) derived from Genotyping by Sequencing were used to analyze genetic patterns among fragmented (1-, 10- and 100-ha) and continuous forests. In the context of the world’s most diverse biome, fragmentation induces marked effects on plant population demography and genetic differentiation. Declines in colonization events in small patches (1- and 10-ha), associated with reduced colony densities, led to accelerated genotypic differentiation (genetic drift) compared to 100-ha fragment and continuous forests. Furthermore, the mating system was related to differential sensitivities to the intensity of fragmentation. Unexpectedly, the unisexual species (hypothesized to be more challenged in terms of spore output) was characterized by higher migration rates among smaller patches than its bisexual counterpart. These results point to the complex and unpredictable patterns revealed when life history strategies, demography, and plant genetic structure are simultaneously evaluated in the context of the long-term effects of reduced landscape connectivity.