Abstract Methane (CH4) and nitrous oxide (N2O) are not only important but also long-lived greenhouse gases. Unfortunately, in Taiwan, although there are some data on CH4 emission from rivers and lakes there is no data about N2O emission from rivers, lakes and coasts. So this study investigated CH4 and N2O distribution in natural waters around Taiwan. In Taiwan, the average CH4 concentration in rivers is about 3082¡Ó12399nM (n=152). The average CH4 concentration in mountain lakes is about 2899¡Ó7291nM (n=51). The average CH4 concentration in lower elevation lakes and reservoirs is about 1825¡Ó2755nM ppmv (n=95). The average CH4 concentration in near-shore waters is about 36.7¡Ó285nM (n=476). The CH4 distribution is rivers> mountain lakes>low-elevation lakes and reservoirs >seawater. In southeastern China, the average CH4 concentration in rivers is about 1029¡Ó2487nM ppmv (n=36). The average CH4 concentration of samples taken from rivers in southeastern China is lower than Taiwan rivers. But the highest CH4 concentration of all samples is in Chih-Kan river of southeastern China (14914nM), due to uneven population distribution as well as different levels of development among cities and suburbs. In Taiwan, the average N2O concentration in rivers is about 32.8¡Ó69.1nM (n=58). In southeastern China, the average N2O concentration in rivers is about 29.7¡Ó9.05nM (n=36). The average N2O concentration in Taiwanese rivers is higher than found in southeastern China. This is likely because farmers in Taiwan use more synthetic fertilizers so the soil becomes full of N element, and then rivers and rains rinse the soil. This process has increased the concentration of N and N2O in rivers. In summer, the average CH4 and N2O concentrations in northern Taiwan Strait are about 3.27¡Ó2.42nM and 7.22¡Ó0.62nM (n=7), respectively; and the average CH4 and N2O fluxes are about 0.17¡Ó0.43£gmol/m2/h and 0.14¡Ó0.26 £gmol/m2/h, respectively. The average CH4 and N2O concentrations in southern Taiwan Strait are about 3.35¡Ó1.97nM and10.31¡Ó2.51nM (n=30), respectively; and the average CH4 and N2O fluxes are about 0.04¡Ó0.09£gmol/m2/h and 0.19¡Ó0.22 £gmol/m2/h, respectively. In winter, the average CH4 and N2O concentrations in northern Taiwan Strait are about 4.74¡Ó1.43nM and 8.41¡Ó0.46nM (n=9), respectively; and the average CH4 and N2O fluxes are about 0.10¡Ó0.14£gmol/m2/h and 0.008¡Ó0.033 £gmol/m2/h, respectively. The average CH4 and N2O concentrations in southern Taiwan Strait are about 4.70¡Ó2.42nM and 8.36¡Ó0.97nM (n=17), respectively; and the average CH4 and N2O fluxes are about 0.17¡Ó0.46£gmol/m2/h and 0.11¡Ó0.12 £gmol/m2/h, respectively. Taiwan Strait is a source of CH4 and N2O regardless of whether it is summer or winter. In summer, the average CH4 and N2O concentrations in the South China Sea are about 4.34¡Ó2.33nM and 8.23¡Ó1.5nM (n=55), respectively; and the average CH4 and N2O fluxes are about 0.33¡Ó0.35£gmol/m2/h and 0.20¡Ó0.24 £gmol/m2/h, respectively. It is a source of CH4 and N2O to the atmosphere. In summer, the average CH4 and N2O concentrations in the West Philippines Sea are about 3.18¡Ó1.57nM and 4.64¡Ó0.39nM (n=60), respectively; and the average CH4 and N2O fluxes are about 0.23¡Ó0.33£gmol/m2/h and -0.28¡Ó0.30 £gmol/m2/h, respectively. It is a source of CH4 but a sink of N2O to the atmosphere.