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Prunus necrotic ringspot virus (PNRSV) is an important virus of stone fruit trees (Prunus sp.). In this study, complete genomic sequences of five PNRSV isolates from P. persica (Pea1 and Pea4), P. avium (Che1 and Che2) and P. cerasifera (P.cerasifera1) in Inner Mongolia of China were determined and analyzed together with other previously published PNRSV sequences in the world. Phylogenetic analysis based on RNA3 sequences divided the five isolates into PV32 (Che1, Che2 and P.cerasifera1) and PV96 (Pea1 and Pea4) group, and re-grouped PNRSV isolates in the world into six groups including a new proposed group (PchMx-Azt) composed of two flowering peach isolates from Mexico. Distinct origins for RNAs of isolate P.cerasifera1 suggested potential reassortment in evolution of PNRSV. In addition, nine recombination events were predicted in RNA1–3 among the isolates. [ABSTRACT FROM AUTHOR]