Apple stem grooving virus (ASGV) is one of the most important viral pathogens infecting pome and stone fruit trees worldwide. In this study, with the complete nucleotide sequence of isolate ASGV-T47, which we generated, molecular variation and recombination in ASGV full genomic sequences worldwide were analyzed. ASGV-T47 shared 79.7-97.6% nucleotide identity with the other isolates worldwide and had the highest identity with an isolate from Japan. Phylogenetic analysis based on whole genome clustered all 16 isolates from around the world into two groups with no correlation to host or geographical origin. Four isolates were detected to be recombinants. Selection pressure estimation indicated that the two codons at positions 1756 and 1798 are under positive selection, while purifying selection is the primary evolutionary dynamics for ASGV.