The modes of molecular evolution of the coat protein (CP) and 3' non-coding region (NCR) were investigated in Bean yellow mosaic virus (BYMV) isolates, including a new pathotype from blue passion fruit. In phylogenetic analysis, the new pathotype did not cluster with pathotypes or host groups described previously. Intraspecific recombinations involving the entire 3'-NCR and a variable portion of the 3'-terminal region of the CP gene were detected between a broad bean isolate and several isolates from monocots. Since the predicted secondary structure of the 3'-NCR correlated mostly with the botanical origin of isolates, a possible role of the 3'-NCR in BYMV host adaptation is proposed and discussed.