In invertebrates, gene body is the primary target of DNA methylation, and only a subset of expressed genes is modified. To reveal methylated and unmethylated gene groups, we investigated distribution of 5mC in the C. intestinalis sperm genome. DNA extracted from sperm was applied to CXXC-affinity purification and deep sequencing (CAP-seq), which is the method specifically enriches unmethylated fraction of DNA using CXXC domain of mouse MBD1, for genome-wide sequencing (Illingworth et al. 2010). We designated body-methylated and unmethylated genes in C. intestinalis sperm cells.