Orchidaceae is one of the largest families in the angiosperms with more than 25,000 species, which displays a great biodiversity resulting from adaptation to diverse habitats (Pridgeon et al. 2005). Genomic information on orchids were mainly focused on Phalaenopsis (Su et al. 2011; Cai et al. 2014), Dendrobium (Yan et al. 2015; Zhang et al. 2016), Cymbidium ensifolium (Li et al. 2013), Cymbidium sinense (Zhang et al. 2013). Cymbidium faberi Rolfe., common named as “Hui Lan”, is one of the oldest and most popular orchids species cultivated in China, which is highly appreciated mainly because of its beautiful flower posture and fragrant aroma (Wolff, 1999). However, large scale commercial production of C. faberi was often hindered due to the long vegetative growth phase (usu. 5–7 years) and difficulties in flowering time control.