The distribution of epiphytes differs between branches within tree crowns as well as within habitats. Where the original forests have been lost, shade coffee plantations can be important refuges for epiphytes, but are not suitable for all species. To understand what affects habitat quality, we transplanted 1440 seedlings each of two orchids, one, Lycaste aromatica, restricted to forests, the other, Jacquiniella teretifolia, common on trees in coffee plantations and in forests. Seedling mortality and growth were compared between three forests, three young and three old coffee plantations to test for differences between habitats and to analyse which habitat features affect growth and mortality. In J. teretifolia there was no clear pattern of habitat effect on mortality (c. 0.08 mo−1), but the production of new shoots was higher in coffee plantations than in forests. In L. aromatica, growth rates as well as seedling mortality increased over time. During the last census growth rates in forests (1.8 mm mo−1) were significantly higher than in old (0.9 mm mo−1) and young (1.2 mm mo−1) coffee plantations, and seedling mortality was about four times higher in old (0.10 mo−1) and young (0.11 mo−1) coffee plantations than in forests (0.025 mo−1), which may explain the natural absence of L. aromatica from coffee plantations. Mortality in L. aromatica at individual sites was negatively correlated with bryophyte cover on branches (Pearson r = –0.75) and positively with lichen cover (r = 0.70) and canopy openness (r = 0.75). Branch cover with non-vascular epiphytes, whether directly responsible by improving the water supply to epiphytes or indicative of differences in microclimate, may be a useful indicator of suitable habitats for vascular epiphytes.