The cotton leaf curl Multan betasatellite encodes an essential pathogenicity determinant involved in induction of disease symptoms. We have shown recently that a recombinant betasatellite with a satellite conserved region derived from the tomato leaf curl betasatellite, is prevalent in the Punjab province and is associated with the breakdown of resistance in cotton to cotton leaf curl disease. We intended to see if the betasatellite that was associated with the first epidemic is still being maintained in some other hosts. We cloned betasatellite from G. barbadense, a cotton species highly susceptible to the disease. We found that both the original and recombinant betasatellite are associated with this cotton species. These findings strengthen our hypothesis that the recombinant betasatellite now prevalent on commercial cotton has been selected due to its ability to cross the host resistance barrier.