DNA methylation is a highly conserved epigenetic mark present in many eukaryotic organisms including plants, animals, and fungi. It plays an important role in the regulation of gene expression. A number of studies have shown its involvement in plant and animal growth and reproduction primary through the processes of genomic imprinting, X-chromsome inactivation, and the silencing of transposons and other repetitive DNA elements. As such, the understanding of DNA methylation has become a major focus of the research conducted during the “post-genomics” era. However, the precise determination of a DNA’s methylation pattern on a genomic scale has posed a challenge especially for those complex genomes. Combining well-established bisulfite conversion chemistry with NextGen sequencing, we have established a robust service platform for analyzing DNA methylation with single base resolution at the genomic scale. The service features a streamlined workflow coupled with a comprehensive bioinformatics pipeline to provide both a consolidated and cost-effective solution for epigenetic analysis of plant and animal genomes. This technology has been used successfully for the analysis of methylomes from many organisms including soybean, mouse, and chicken. Additional analyses of other species are ongoing. Those data should provide a means to understanding how environment as well as other factors may alter an organism’s fitness through heritable changes in epigenetic gene expression.