In addition to habitat loss and fragmentation, habitat degradation can have important consequences for biodiversity and population persistence, including effects on ecological and genetic processes beyond decreased demographic viability and the loss of genetic variation. Particularly interesting is the potential for evolutionary changes and adaptation to degraded habitats, that can affect population viability even in the short-term. Here, I explore how environmental changes after habitat degradation affect the evolutionary dynamics of populations of the rainforest cycad Zamia fairchildiana, specifically how habitat degradation affects gene dispersal, inbreeding, directional selection, and genotype-by-environment interactions, and the potential for genetic differentiation between populations. Colonies of Z. fairchildiana showed little genetic differentiation in neutral molecular markers across study sites, thus can be considered as subpopulations. Subpopulations in the disturbed habitat are experiencing different environmental conditions when compared to subpopulation in their native habitat. Disturbed-habitat subpopulations showed a faster life-history. This faster life history is associated with a weaker spatial genetic structure and higher levels of inbreeding in the disturbed-habitat subpopulations. In addition, higher light availability in the disturbed habitat seems to be a major agent of selection on traits like leaf production that have the potential to respond to selection in these subpopulations. Different traits were under selection in the native-habitat subpopulations, suggesting the potential for genetic differentiation between native and disturbed-habitat subpopulations. Genotype by environment interactions in seed germination and seedling survival, in response to light and water availability, further suggested that subpopulations can adaptively diverge between habitats, but the relative role of genetic and environmental factors, particularly maternal effects, on the magnitude and rate of genetic differentiation between subpopulations remains to be evaluated. These results suggest that habitat degradation can have important consequences for the evolutionary dynamics of populations of this cycad, not necessarily typical of habitat loss and fragmentation. This study identified factors and processes important for population persistence in degraded habitats, but population responses to habitat degradation are complex. Thus further studies and long-term experiments are required for better understanding the effects of habitat degradation on population viability.