The pathogenic watermelon mosaic virus (WMV) causes severe crop losses and threatens cucurbits production worldwide. This study presents the first sequenced genome of WMV from Iraq and the second from Iran. The near-complete genome sequences of Iranian (In) and Iraqi (Iq) isolates were, respectively, 9999 and 10,041 nucleotides in length, excluding the 3′-terminal poly(A) tail. WMV-Iq and WMV-In shared nucleotide identities of 92.61–96.32% with those of 30 worldwide representative WMV isolates in GenBank and identities of 93.04–93.90% with a previously reported Iranian isolate IR02-54. Phylogenetic analysis based on the genomic sequences clustered all 32 isolates into seven groups (G1–G7), in which WMV-Iq and WMV-In clustered alongside 12 isolates from Asia, Europe, and America in group G1. Phylogenetic analysis of nucleotide sequences of the coat protein gene of WMV isolates resolved into five phylogroups (I–V) and both isolates, WMV-Iq and WMV-In, clustered together with isolates in group I and contain the N-terminal KEA motif, which is the characteristic of group I isolates. Our results show that WMV-Iq and WMV-In are recombinant isolates with multiple recombination events detected across the genome. Symptom intensity of WMV isolates in experimental hosts was variable and depended upon the host species, virulence of isolates, and environmental conditions.

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