Epiphytes are diverse and important elements of tropical forests, but as canopy-dwelling organisms, they are highly vulnerable to deforestation. To assess the effect of deforestation on epiphyte diversity and the potential for epiphyte conservation in anthropogenically transformed habitats, we surveyed the epiphytic vegetation of an Ecuadorian cloud forest reserve and its surroundings. Our study was located on the western slopes of the Andes, a global center of biodiversity. We sampled vascular epiphytes of 110 study plots in a continuous primary forest; 14 primary forest fragments; isolated remnant trees in young, middle-aged, and old pastures; and young and old secondary forests. It is the first study to include all relevant types of habitat transformation at a single study site and to compare epiphyte diversity at different temporal stages of fragmentation. Epiphyte diversity was highest in continuous primary forest, followed by forest fragments and isolated remnant trees, and lowest in young secondary forests. Spatial parameters of habitat transformation, such as fragment area, distance to the continuous primary forest, or distance to the forest edge from inside the forest, had no significant effect on epiphyte diversity. Hence, the influence of dispersal limitations appeared to be negligible or appeared to operate only over very short distances, whereas microclimatic edge effects acted only in the case of completely isolated trees, but not in larger forest fragments. Epiphyte diversity increased considerably with age of secondary forests, but species assemblages on isolated remnant trees were impoverished distinctly with time since isolation. Thus, isolated trees may serve for recolonization of secondary forests, but only for a relatively short time. We therefore suggest that the conservation of even small patches of primary forest within agricultural landscape matrices is essential for the long-term maintenance of the high epiphyte diversity in tropical cloud forests.