We developed an inexpensive methylation-based capture method for enriching host DNA from noninvasively obtained fecal samples. We demonstrate that the enrichment is robust, efficient, and compatible with downstream library preparation methods, including complexity-reduction approaches for massively parallel sequencing. Because feces are widely available and convenient to collect, our method empowers researchers to explore genomic-scale population-level questions in organisms for which invasive sampling is challenging or undesirable.