During the last decade, the leafhopper transmitted Wheat dwarf virus (WDV) has become a serious problem both in northwestern China and Hungary. In order to study the molecular diversity and population structure of WDV in these two countries, 39 Chinese isolates and 16 Hungarian isolates were collected from different regions of China and Hungary, and their genomes were sequenced. All isolates belonged to the wheat strain of WDV and showed limited genetic diversity. The highest and lowest nucleotide sequence identities among isolates from China and Hungary were 99.9 and 90%, respectively. In all isolates, the lowest nucleotide sequence identity was 89.5% between MO10-1 and KP10-5, which were collected from Martonvàsàr and Kompolt, Hungary. Phylogenetic analyses showed the genome sequences of 55 WDV isolates belong to two big clades, but no clear correlation to geographical location. Population difference analyses indicated that the Chinese and Hungarian WDV populations have no significant difference. The regions in WDV genome with relatively low nucleotide diversities represented protein coding regions suggested that these regions evolved under negative selection, and might be one of the causes restricting the number of genetic variants. During the last decade, the leafhopper transmitted wheat dwarf virus (WDV) has become a serious problem both in northwestern China and Hungary. In order to study the molecular diversity and population structure of WDV in these two countries, 39 Chinese isolates and 16 Hungarian isolates were collected from different regions of China and Hungary, and their genomes sequenced. All isolates belonged to the wheat strain of WDV and showed limited genetic diversity. The highest and lowest nucleotide sequence identities among isolates from China and Hungary were 99.9 and 90% respectively. All isolates, the lowest nucleotide sequence identity was 89.5% between MO10-1 and KP10-5, which were collected from Martonvàsàr and Kompolt, Hungary. Phylogenetic analyzes showed the genome sequences of 55 WDV isolates belong to two big clades, but no clear correlation to geographical location. Population difference analyzes have shown that the Chinese and Hungarian WDV populations have no signific ant difference. The regions in WDV genome with relatively low nucleotide diversities represented protein coding regions suggested that these regions evolved under negative selection, and might be one of the causes restricting the number of genetic variants.