We have determined the complete genome sequence of an apple stem pitting virus isolate (ASPV, genus Foveavirus) from China, providing a new genome sequence of an ASPV isolate from apple trees. Nucleotide identities and phylogenetic relationships among this and another eleven complete sequences of ASPV isolates largely differed according to the coding regions of the genome analysed, suggesting the possible occurrence of recombination. Using recombination-detection programs, multiple recombination events throughout the ASPV genome were predicted to occur among isolates, regardless of their host species. Our analyses suggest that pervasive genome recombination drives the evolution and genetic diversity of ASPV.