In contrast to mammals where DNA methylation occurs near exclusively at CG dinucleotides, all cytosines of plant genomes can be methylated irrespective to the sequence context, including the symmetrical CG and CHG sequence contexts, and the nonsymmetrical CHH sequence context. Plant genomes do not present CG islands as found in mammalian genomes where a high frequency of CG can be observed at some promoter regions. So far, the methylome of several plants has been described showing variations of both methylation levels between plants, which ranged from 5% in Arabidopsis thaliana to more than 30% in corn, but also of the proportion of methylated cytosines in the CG, CHG, and CHH sequence contexts. DNA methylation was shown to have important roles in the development of many organisms including plants. In this later case, DNA methylation is involved in the regulation of flowering time, flower sex determination, seed development, or fruit ripening. To date, a wide range of low to high resolution methods initially developed for animal genomes allow the analysis of DNA methylation at specific loci or globally of whole genomes. Indeed, part of these methods is not applicable to plants due to the specificities of their methylome; however, some have been successfully modified to overcome the complexity of plant DNA methylation. In this chapter, we describe an exhaustive list of methods devoted to the locus-specific analysis of DNA methylation which have proven to be applicable to plant genomes and their potential use in high throughput screening of plant population.< Réduire