Here, we describe a method capable of filtering the hypomethylated part of plant genomes, the so-called hypomethylome. The principle of the method is based on the filtration and sequence analysis of small DNA fragments generated by methylation-sensitive four-cutter restriction endonucleases, possessing ((5me))CpG motifs in their recognition sites. The majority of these fragments represent genes and their flanking regions containing also regulatory elements-the gene space of the genome. Besides the enrichment of the gene space, another advantage of the method is the simultaneous depletion of repetitive elements due to their methylated nature and its easy application on complex and large plant genomes. Additionally to the wet lab procedure, we describe how to analyze the data using bioinformatics methods and how to apply the method to comparative studies.