The full-length sequences of 13 isolates of Watermelon mosaic virus (WMV, genus Potyvirus) belonging to the three main molecular groups defined at the capsid level were obtained and compared to 4 sequences available in databases. Many isolates presented evidence for intraspecific recombination, particularly between molecular groups 1 and 2. Most isolates had different recombination breakpoints suggestive of multiple independent recombination events. The breakpoints were for the most part located between the C-terminal half of the HC-Pro coding region and the N-terminal part of the CI coding region. There was no evidence for positive selection in the WMV genome.