Abstract: Orchidaceae is one of the largest families of flowering plants. DNA molecular marker techniques have been used in taxonomy, phylogenetic analysis between different species or varieties,and conservation. Orchidaceae has highly specialized morphological, structural, and physiological characteristics，it is an ideal material to study flower pigmentation and ovule initiation and development. In vitro flowering techniques of orchids provide a model system to study inflorescence differentiation and development. Flavonoid pathway was regulated by CHS and DFR gene in orchids.Flower bud formation and early flowering were controlled by DOH1 gene in Dendrobium. ACC synthase gene and PHAL.039 gene were most likely important regulators involved in ovule tissue initiation and development in Phalaenopsis. Genetic transformation has been reported in Phalaenopsis spp., Cymbidium spp., Oncidium spp., Dendrobium spp.， Doritis spp., and Vanda spp .Transgenic plants were produced from protocorm by bombardment or Agrobacterium mediated transformation.