This study quantitatively estimates the spatial distribution of anthropogenic methane sources in the United States by combining comprehensive atmospheric methane observations, extensive spatial datasets, and a high-resolution atmospheric transport model. Results show that current inventories from the US Environmental Protection Agency (EPA) and the Emissions Database for Global Atmospheric Research underestimate methane emissions nationally by a factor of ∼1.5 and ∼1.7, respectively. Our study indicates that emissions due to ruminants and manure are up to twice the magnitude of existing inventories. In addition, the discrepancy in methane source estimates is particularly pronounced in the south-central United States, where we find total emissions are ∼2.7 times greater than in most inventories and account for 24 ± 3% of national emissions. The spatial patterns of our emission fluxes and observed methane–propane correlations indicate that fossil fuel extraction and refining are major contributors (45 ± 13%) in the south-central United States. This result suggests that regional methane emissions due to fossil fuel extraction and processing could be 4.9 ± 2.6 times larger than in EDGAR, the most comprehensive global methane inventory. These results cast doubt on the US EPA’s recent decision to downscale its estimate of national natural gas emissions by 25–30%. Overall, we conclude that methane emissions associated with both the animal husbandry and fossil fuel industries have larger greenhouse gas impacts than indicated by existing inventories.