The role of epigenetic alterations as a contributor to intraspecific variation for transcription levels is unclear. We have studied the functional targets of the maize chromomethylase ZMET2 in multiple inbred lines to determine whether the targets for this chromomethylase are conserved or variable within the species. DNA microarrays were interrogated with RNA from the inbred lines B73 and Mo17, and from near-isogenic derivatives containing the loss-of-function allele zmet2-m1. A set of 126 genes that displayed statistically significant differential expression in zmet2 mutants relative to wild type plants in at least one of the two genetic backgrounds were identified. Analysis of the transcript levels in both wild type and mutant individuals revealed that only ten percent of these genes exhibited differential expression in both B73 and Mo17 genetic backgrounds. Further analysis was performed for seven genes that are normally silent in B73 but expressed in B73 zmet2-m1 mutant lines and in wild type Mo17. Mapping experiments confirm that the expression difference in B73 relative to Mo17 is caused by cis-acting regulatory variation. Methylation sensitive PCR and bisulphite sequencing were used to demonstrate the presence of CpNpG methylation in the B73 allele that is absent in the zmet2-m1 mutant and in wild-type Mo17 for five of these genes. Each of these five genes exist in methylated, transcriptionally silent states in some inbred lines and unmethylated, expressed states in other maize inbred lines, providing evidence for natural variation in epigenetic states for some maize genes.