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Rootstocks play a vital role in regulating the environmental adaptability and controlling the growth and development of apple trees. M9T337, an excellent apple rootstock widely used in commercial orchards, could confer dwarf tree architectures, early fruiting and suitability for high-density planting. However, the rooting ability of M9T3337 is low when it is vegetatively propagated, and researchers have not yet established an efficient micropropagation system. The present study systematically evaluated the multiplication in adventitious shoots and the in vitro formation of adventitious roots to determine the effects of the culture media and plant growth regulators of M9T337 and a rapid micropropagation system was developed. For the shoot multiplication, the highest multiplication index of 3.93 was obtained on Murashige and Skoog (MS) media supplemented with 2.0 mg/L 6-BA, 0.1 mg/L NAA and 0.3 mg/L GA3 from 12 combinations of 6-BA and NAA. Stronger and taller adventitious shoots were grown on MS supplemented with 1.8 mg/L 6-BA and 0.5 mg/L NAA. The optimal media with 100% rooting was obtained using ½ MS supplemented with 0.3 mg/L IBA or MS supplemented with 0.6 mg/L IBA for the rooting induction, resulting in mean rooting numbers of 13.00 and 11.33, respectively. Additionally, the effect on rooting of adding 0.3 mg/L IBA or not on the 1/2 MS and MS media was compared; the results suggested that an appropriate IBA concentration was the key to successful rooting. The rooted plantlets were acclimatised in a shaded greenhouse with an 84% survival rate. The established micropropagation system could be used for the rapid propagation of M9T337 for commercial production.