The invention relates to paclitaxel genome shuffling bacterial strain HDFS4-26 and a seed selection method of high yield paclitaxel bacterial strain, which belongs to the paclitaxel genome shuffling bacterial strain and the seed selection method of the paclitaxel engineering bacterial strain and solves the problem that the paclitaxel output of the bacterial strain which can be used in the paclitaxel microorganism fermentation at present is still relatively low. The paclitaxel genome shuffling bacterial strain HDFS4-26 is nodulisporium sylviforme and belongs to the nodulisporium and is preserved in the China Center for Type Culture Collection, the preservation date is February 28, 2008, the preservation number is CCTCC M 208026. The seed selection method of the high yield paclitaxel bacterial strain adopts firstly, the protoplast preparation; secondly, the inactivation of the protoplast; thirdly, the interfusion of the protoplast; fourthly, the regeneration of the protoplast; fifthly, the genome shuffling and sieving, therefore to obtain the high yield paclitaxel bacterial strain. The paclitaxel output of the bacterial strain HDFS4-26 is 516.37ug/L. The seed selection method of the high yield paclitaxel bacterial strain provided by the invention is simple, the effect is good, and the paclitaxel genome shuffling bacterial strain HDFS4-26 and the seed selection method of high yield paclitaxel bacterial strain lay the foundation of industrial production of bacterial strain providing high yield paclitaxel.