It is estimated that lakes are responsible for up to 16% of global methane (CH 4 ) emissions. Studying the CH 4 concentrations and emissions in these environments is important to estimate the total regional production of CH 4 and to understand the main factors related to these emissions. The aim of this study was to measure the CH 4 emissions from two shallow polymictic lakes in southern Brazil and to evaluate the roles of temperature and trophic level in increasing these emissions. Temperature was positively correlated with CH 4 concentration in the water column, bubble emissions and diffusion. Both lakes exhibited significant seasonal differences in water-column and sediment methane concentrations and diffusion. The eutrophic lake produced more bubble emissions [6868.95 (±7645.97) μmol m −2 d −1 in winter and 11,251.10 (±10,160.92) μmol m −2 d −1 in summer]. Water-column and sediment concentrations [19.92 (±11.74) μmol L −1 and 1727.85 (±1581.19) μmol g −1 , respectively)] and diffusion [27,549.94 (±18,258.15) μmol m −2 d −1 ] were also higher in summer than in winter in both lakes. All measured parameters were higher in the eutrophic lake, highlighting the maintenance of aquatic ecosystems in a low trophic state. Based on bubble emissions, the oligo-mesotrophic lake released an estimated 3142.8 g ha −1 yr −1 of CH 4 , while the eutrophic lake contributed 287,868.6 g ha −1 yr −1 . Estimates of diffusive flux were higher: 41,832 g ha −1 yr −1 in summer for the oligo-mesotrophic lake and 1388.52 kg ha −1 yr −1 for the eutrophic lake. Our results show that shallow aquatic subtropical ecosystems are potential sources of atmospheric methane, and their contribution to global warming must be taken into account.