BackgroundApple stem grooving virus (ASGV) has a wide host range, notably including apples, pears, prunes and citrus. It is found worldwide.MethodIn this study, two near complete genomes, and seven coat protein (CP) sequences of Iranian isolates from apple were determined. Sequences added from GenBank provided alignments of 120 genomic sequences (54 of which were recombinant), and 276 coat protein genes (none of them recombinant).ResultThe non-recombinant genomes gave a well supported phylogeny with isolates from diverse hosts in China forming the base of the phylogeny, and a monophyletic clade of at least seven clusters of isolates from around the world with no host or provenace groupings among them, and all but one including isolates from China. The six regions of the ASGV genome (five in one frame, one − 2 overlapping) gave significantly correlated phylogenies, but individually had less statistical support. The largest cluster of isolates contained those from Iran and had isolates with worldwide provenances, and came from a wide range of mono- and dicotyledonous hosts. Population genetic comparisons of the six regions of the ASGV genome showed that four were under strong negative selection, but two of unknown function were under positive selection.ConclusionASGV most likely originated and spread in East Asia in one or more of various plant species, but not in Eurasia; the ASGV population of China had the greatest overall nucleotide diversity and largest number of segregating sites.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12985-023-02075-2.