During the transition from vegetative growth to reproductive growth, MADS-box family genes play important roles in regulating floral organ specification, development and evolutionary in higher plants (Weigel and Meyerowitz 1994; Purugganan et al. 1995; Münster et al. 1997). Although conserved flowering pathways and multiple key genes were revealed in model plants, there is limited information of C. faberi, the very unique and important plant species featured with a 5–7 year-long vegetative growth phase. Unlike most tropical orchids (e.g. Phalaenopsis and Cattleya), C. faberi flowers are not brightly showy but of strong aromas to attract pollinating insects. It is of strong interest for orchid breeders to improve the appearance of its flower size, color and shape with uncompromised aromas. The flowers of C. faberi are zygomorphic consisting of four whorls: The first whorl is comprised of the petal-like sepals, the second whorl is of two petals and one highly specialized labellum in the middle, the third whole is of stamens, and fourth whorl is of pistils in the form a highly specialized united gynostemium (Rudall and Bateman 2002). The well-known ABC model clarify that floral development is determined by five kinds of floral organ identity genes in diverse plant groups (Coen and Meyerowitz 1991; Weigel and Meyerowitz 1994). Sepal formation is specified by the expression of A-class function genes. Expression of AB and BC determine the development of petals and stamen formation, respectively. The development of carpel is determined by C-class genes function alone, and D-class genes specify ovules. While class E function redundantly specify petals, stamens, and carpels as well as floral determinacy (Pelaz et al. 2000, 2001; Anusak et al. 2003). The floral morphology of orchid species is unique with gynostemium, labellum and resupination caused by 180° torsion of the pedicel (Rudall and Bateman 2002). ‘The Perianth (P) code’ clarifies the mechanisms of sepal/petal/lip determination in Oncidium and Phalaenopsis orchids. The competition between different APETALA3/AGAMOUS-LIKE6 (AP3/AGL6) homologues determines the formation of the complex perianth patterns in orchids. The formation of sepal/petal were specified by the higher-order heterotetrameric SP (sepal/petal) complex (OAP3-1/OAGL6-1/OAGL6-1/OPI), whereas the lip formation required the L (lip) complex (OAP3-2/OAGL6-2/OAGL6-2/OPI) exclusively (Hsu et al. 2015). Other MADS-box function genes participating in the sepal and petal development were also isolated from Dendrobium madame, D. crumenatum, Oncidium Gower Ramsey (Yu et al. 2000, 2002; Hsu and Yang 2002; Hsu et al. 2003; Xu et al. 2006). Genes involved in flower identity and floral organ specification are still unknown in C. faberi yet.