Brachypodium distachyon which characters a small genome size, a short lifecycle, simple cultivation condition, and high transformation efficient is one of most popular model plants recently. The International Brachypodium Initiative (IBI) just sequenced the whole genome in February 2010. The SGT1 and RAR1 genes are pretty important and well conserved genes related the plant resistant disease function. RNA interference (RNAi) is an excellent and major method to study the genes’ function of plants nowadays. In this paper, we used the new powerful cloning system called Gateway Cloning to generate the high-throughout inducible RNAi gene silence vectors for these two important disease related genes in Brachypodium distachyon. Gateway Cloning system is a time-saving, easy to operating, and high efficient molecular cloning technology. It concluded two steps which called BP reaction and LR reaction respectively. At the same time we also used the Gateway Cloning to generate the protein TAP-tag fusion vectors which can be used for the study of the purification the SGT1 and RAR1 proteins and their interactive proteins in this new model plant Brachypodium distachyon. Finally we used the Agrobacterium-mediated transformation system (ATMT) to transform these RNAi and TAP-tag fusion vectors into Brachypodium distachyon genetype Bd21, and got the RNAi TAP-tag fusion plant transformants which can be used for further studying the function of these two genes related disease resistance in Brachypodium distachyon in future.