Tomato yellow leaf curl China virus (TYLCCNV) Y10 isolate (Y10) and Tobacco curly shoot virus (TbCSV) Y35 isolate (Y35), both obtained from Yunnan Province, were each found to be associated with a distinct species of satellite DNA (DNA β). Here, we demonstrate that both Y10 DNA β (Y10β) and Y35 DNA β (Y35β) were stably trans-replicated by the noncognate Begomovirus, although the noncognate DNA β accumulated in plants at a lower level than did the cognate DNA β. In Nicotiana benthamiana and N. glutinosa plants agroinoculated with Y10+Y10β+Y35β or with Y35+Y35β+Y10β, all components accumulated in the early stages of infection but, at later stages, the noncognate DNA β decreased in relative concentration and was undetectable at 80 to 120 days after inoculation. The helper viruses and cognate DNA β species persisted at higher levels throughout the experiments. When the initiation codon of the βC1 gene of the cognate DNA β was mutated, the dominance of the cognate over the noncognate DNA β in mixed infections was unimpaired. These results imply that the cognate DNA β competes with the noncognate DNA β and that the ability for selective maintenance of DNA β is not controlled by the βC1 protein.