The micromorphology of a seed is linked to its dispersal and germination, but evolutionary and ecological aspects in Orchidaceae remain unclear. We investigated the seed characters of Paphiopedilum and Cypripedium that might be associated with life form and involved in possible ecological adaptations. A phylogenetic comparative analysis of nine seed micromorphological characters was performed in 24 species from two genera with close phylogenetic relationships but significant differences in their ecological characteristics. Species within Paphiopedilum had larger embryos and a smaller percentage of air space (AS) than those of Cypripedium species. Compared with 16 terrestrial species, two epiphytic Paphiopedilum species had larger embryos and smaller AS. Those larger embryos might ensure more successful seedling establishment while the higher amount of air space in both terrestrial Paphiopedilum and Cypripedium may increase seed buoyancy and enable them to disperse over longer distances. Whereas AS and seed length (SL) are phylogenetically conservative, most other characters examined here had weak signals, indicating clear convergent evolution. Across species, SL was positively correlated with AS, indicating a high degree of seed size–dispersal coordination. These findings may imply a trade-off of seed characters in relation to the possible ecological adaptations required for seedling establishment versus dispersal.