Approximately 14% of all fern species have physiologically active chlorophyllous spores that are much more short-lived than the usual and dormant achlorophyllous spores. Most chlorophyllous-spored species (70%) are epiphytes, and these account for almost 37% of all epiphytic ferns. Chlorophyllous-spored ferns are also overrepresented among species in habitats with waterlogged soils, of which nearly 60% have chlorophyllous spores. Ferns in these disparate habitat types are also united by a low incidence of mycorrhizal associations. We, therefore, hypothesize that autotrophic chlorophyllous spores represent an adaptation of ferns to habitats with scarce mycorrhizal associations. We evaluated the evolution of chlorophyllous spores and mycorrhizal associations in ferns and their relation to habitat type using phylogenetic comparative methods. We found that chlorophyllous spores and the absence of mycorrhizal associations are strongly associated with epiphytic and waterlogged habitats. Transition rates to epiphytic and waterlogged habitats are 200-fold higher in species with chlorophyllous spores compared to achlorophyllous lineages. Spore type and mycorrhizal associations appear to play important roles in the radiation of ferns into different habitat types. Future work should focus on clarifying the functional significance of these associations.