In this study, we isolated and characterized the function of a GLOBOSA/PISTILLATA-like gene, PeMADS6, from a native Phalaenopsis species, P. equestris. Southern blot analysis showed PeMADS6 as a single copy in the Phalaenopsis genome. Results of the determination of temporal and spatial expression showed that PeMADS6 was expressed and thus participated in the development of the sepals, petals, labellum and column in Phalaenopsis. Further confirmation of the expression pattern of PeMADS6 was carried out with in situ hybridization. Repressed expression of PeMADS6 in the orchid ovary was found to be pollination regulated, which suggests that the gene may have an inhibitory effect on the development of the ovary or ovule. In addition, auxin acted as the candidate signal to regulate the repression of PeMADS6 expression in the ovary. Furthermore, the flowers of transgenic Arabidopsis plants ectopically overexpressing PeMADS6 showed the morphology of petaloid sepals, with a 3- to 4-fold increase in flower longevity. Concomitantly, delayed fruit maturation was also observed in the transgenic Arabidopsis, which is consistent with the inhibitory effect of PeMADS6 on the development of the ovary. Thus, as a B-function gene, PeMADS6, not only specifies floral organ identity but has functions in flower longevity and ovary development in orchids.