The 3' noncoding aminoacylatable regions of the three genomic RNAs of brome mosaic (BMV) and cucumber mosaic (CMV) viruses are highly conserved and exhibit extensive similarities in their primary and secondary structures. To investigate the functional significance of these conserved features, the 3' 186 nucleotide sequence of Fny-CMV RNA3 was incorporated into the 3' end of full-length genomic BMV RNA2 and RNA3 and their replicative competence and infectivity were examined in barley protoplasts and Chenopodium quinoa plants, respectively. In barley protoplasts, functional replicase provided by wild-type BMV RNAs 1 and 2 successfully interacted with the CMV 3' end when present on RNA3 and resulted in the proliferation and accumulation of chimeric progeny RNA3 and RNA4. In contrast, when CMV 3' end sequences were present on RNA2 no amplification of chimeric RNA occurred. Inoculation of chimeric RNAs to C. quinoa revealed that systemic infections were derived from the selection of higher fitness recombinant sequences over lower fitness chimeric RNAs.