DNA methylation is important for the epigenetic silencing of repetitive DNA in plant genomes. For satellite DNAs, as a major class of repetitive DNA, knowledge about their cytosine methylation status is scarce. One reason is that arrays of tandemly arranged sequences are usually collapsed in NGS assemblies. We applied strategies to overcome this limitation and quantified the cytosine methylation level and patterns in three satellite families of sugar beet (Beta vulgaris) which differ in their abundance, chromosomal localization and monomer size. We visualized methylation levels along pachytene chromosomes with respect to small satellite loci at maximum resolution using chromosome-wide fluorescent in situ hybridization complemented with immunostaining and super-resolution microscopy. We found that many satellite monomers display only low methylation. To investigate the methylation at nucleotide level we performed bisulfite sequencing of 1,569 satellite sequences. We found that the level of methylation of cytosine strongly depends on the sequence context: Cytosines in the CHH motif show lower methylation (44% - 52%), while CG and CHG motifs are more strongly methylated. This affects overall methylation of satellite sequences because CHH occurs frequently while CG and CHG are rare or even absent in the investigated satellite arrays. Evidently, CHH is the major target for the modulation of the cytosine methylation level of adjacent monomers within individual arrays and contributes to their epigenetic function. This strongly indicates that the asymmetric cytosine methylation plays a role in the epigenetic modification of satellite repeats in plant genomes.This article is protected by copyright. All rights reserved.