In a previous study on doubly transformed tobacco plants, we observed the unexpected inactivation in trans of T-DNA-I (encoding KanrNOS) following the introduction into the same genome of an unlinked copy of T-DNA-II (encoding HygrOCS). This inactivation, which probably resulted from interactions between homologous regions on each T-DNA, was correlated with methylation in the nospro, which controlled the expression of both the nptII and nos genes. In this paper, we show that the inactivation and methylation of the nos(pro)nptII gene in the presence of a suppressor T-DNA-II locus can be either complete (epistasis) or partial (cellular mosaicism). In plants showing partial suppression, the strength of the Kanr phenotype, which apparently reflected the proportion of cells expressing the nptII gene, was inversely correlated with the degree of methylation of the nos(pro). The extent of nos(pro) methylation decreased progressively in successive generations as suppressor T-DNA-II loci were crossed out. The strength of the Kanr phenotype was improved and nos(pro) methylation was less extensive in first generation Kanr progeny obtained from outcrossing with untransformed tobacco than from self-fertilization.