The Wassilewskija (WS) strain of Arabidopsis has four PAI genes at three sites: an inverted repeat at one locus plus singlet genes at two unlinked loci. These four genes are methylated over their regions of DNA identity. In contrast, the Columbia (Col) strain has three singlet PAI genes with no methylation. To test the hypothesis that the WS inverted repeat locus triggers methylation of unlinked identical sequences, we introduced this locus into the Col background by genetic crosses. The inverted repeat induced de novo methylation of all three unmethylated Col PAI genes, with methylation efficiency varying with the position of the target locus. These results, plus results with inverted repeat transgenes, show that methylation is communicated by a DNA/DNA pairing mechanism.