Xanthomonas oryzaepv.oryzae(Xoo) is a causative agent of rice bacterial blight (BB). In 2020–2022, BB re-emerged, and there was a break out in the Yangtze River area, China. The pandemicXoostrain, LA20, was isolated and identified from cultivar Quanyou1606 and demonstrated to be the Chinese R9Xoostrain, which is able to override the widely adoptedxa5-,Xa7- andxa13-mediated resistance in rice varieties in Yangtze River. Here, we report the complete genome of LA20 by PacBio and Illumina sequencing. The assembled genome consists of one circular chromosome of 4,960,087 bp, sharing 99.65% sequence identity with the traditional representative strain, YC11 (R5), in the Yangtze River. Comparative genome analysis of LA20 and YC11 revealed the obvious variability inTalgenes (the uppermost virulence determinants) in numbers and sequences. Particularly, sixTalgenes were only found in LA20, but not in YC11, among whichTal1b(pthXo1)/Tal4(pthXo6), along with the lost one,pthXo3(avrXa7), might be the major factors for LA20 to overcomexa5-,Xa7- andxa13-mediated resistance, thus, leading to the resurgence of BB. This complete genome of the new pandemicXoostrain will provide novel insights into pathogen evolution, the traits of pathogenicity on genomic level and the epidemic disease status in China.