Pork production is one of the most important agricultural activities in the United States, accounting for about $20 billion sales in 2011. Swine farms in upper Midwestern states of Minnesota, Iowa and Illinois are primarily designed with deep pit storage of manure under the pig barns, and manure is pumped out of these barns one to two times per year for land application. In recent years, it has been observed that a layer of foam would unexpectedly develop on the manure surface that is stored in these pits. This manure foaming has becomes a growing concern in the US swine industry because it traps a significant amount of methane gas, which is explosive under relatively high concentration, causing incidents of swine worker injuries and massive loss of living pigs by barn explosions and flash fires. No specific strategy has been developed to prevent the foaming and some swine producers are adding anti-foaming agents to provide a short term solution to prevent flash fires and explosions. Since no explanation of this manure foaming has been published, this study hypothesized several theories and then conducted related research. One hypothesis is that filamentous bacteria, which are considered the reason of foaming in municipal wastewater treatment systems, are the cause of this problem. Another hypothesis is that dried distillers grains with solubles (DDGS), an ethanol production by-product that is replacing corn and soybean in pig’s diet, are the cause of this problem. To verify these two hypotheses, microbial identification and chemical property analysis were carried out on different manure samples. This study provides experimental results to test these hypotheses, and more importantly provides ideas for the mitigation of the foaming issue. The research is expected to save labor and costs in the control of manure pit, and provide a safe environment for swine producer working and pigs living in these barns.