Development of an efficient and cost-effective doubled haploid production system and genetic transformation system are the prerequisite to initiate haploid breeding and genetic modification in flax respectively. Pre-culturing anthers on a high osmotic, high auxin and high mineral salt concentration for a period of time before transfer to a low osmotic, low auxin and low salt concentration significantly increased the overall efficiency of regeneration or anther efficiency than directly culturing anthers on a low osmotic, low auxin and low salt concentration medium. This culture procedure also dramatically reduced the frequency of shoot regeneration from somatic cells in anther culture. Using this procedure, a highly efficient anther culture-derived callus based transformation system was developed. The transformation efficiency of anther culture-derived callus based transformation system was four times higher than the best reported transformation efficiency using hypocotyls as the ex-plants in Agrobacterium tumefaciens based transformation system or particle bombardment based transformation system. The frequency of escape in anther culture-derived callus based transformation system was one third of that in hypocotyl-based transformation system using A. tumefaciens or one half using particle bombardment. This very high efficient transformation system will prove to be very valuable in basic research for gene discovery and practical applications in genetic engineering for improved traits.