Cytosine methylation is an epigenetic modification that plays a role in regulation of transcription. Methylation, particularly at promoter CpG-islands, can lead to silencing of the associated gene. In mammals, DNA methylation has several well characterized regulatory functions, including the chromosome-wide epigenetic silencing of the X chromosome (called X-chromosome inactivation; XCI). XCI is part of a dosage compensation system in therian (eutherian and marsupial) mammals that results in almost equal average transcriptional output from the X chromosome between the sexes. DNA methylation is a late and stabilizing step in maintaining transcriptional silence of the X in eutherian mammals, but there are limited detailed data about DNA methylation in marsupials, monotreme and birds. Here we present a genome wide analysis DNA methylation in non-eutherian representatives from three amniote vertebrate lineages, each with independently evolved dosage compensation systems.