DNA methylation is a chromatin modification that is often associated with the exciting and sometimes unpredictable patterns of inheritance that can unfold with epigenetic phenomena. The stability and heritability of DNA methylation patterns perhaps allow us to utilize DNA methylation profiles to distil the suite of potentially functional elements in large crop genomes. Here, we discuss the potential and possible ways to use the absence of DNA methylation to identify potential regulatory regions within intergenic sequences and the presence of DNA methylation to identify pseudogenes.