Abstract. The Amazon plays a critical role in global atmospheric budgets of methane (CH₄) and nitrous oxide (N₂O). However, while we have a relatively good understanding of the continental-scale flux of these greenhouse gases (GHGs), one of the key gaps in knowledge is the specific contribution of peatland ecosystems to the regional budgets of these GHGs. Here we report CH₄ and N₂O fluxes from lowland tropical peatlands in the Pastaza–Marañón foreland basin (PMFB) in Peru, one of the largest peatland complexes in the Amazon basin. The goal of this research was to quantify the range and magnitude of CH₄ and N₂O fluxes from this region, assess seasonal trends in trace gas exchange, and determine the role of different environmental variables in driving GHG flux. Trace gas fluxes were determined from the most numerically dominant peatland vegetation types in the region: forested vegetation, forested (short pole) vegetation, Mauritia flexuosa-dominated palm swamp, and mixed palm swamp. Data were collected in both wet and dry seasons over the course of four field campaigns from 2012 to 2014. Diffusive CH₄ emissions averaged 36.05 ± 3.09 mg CH₄–C m⁻² day⁻¹ across the entire dataset, with diffusive CH₄ flux varying significantly among vegetation types and between seasons. Net ebullition of CH₄ averaged 973.3 ± 161.4 mg CH₄–C m⁻² day⁻¹ and did not vary significantly among vegetation types or between seasons. Diffusive CH₄ flux was greatest for mixed palm swamp (52.0 ± 16.0 mg CH₄–C m⁻² day⁻¹), followed by M. flexuosa palm swamp (36.7 ± 3.9 mg CH₄–C m⁻² day⁻¹), forested (short pole) vegetation (31.6 ± 6.6 mg CH₄–C m⁻² day⁻¹), and forested vegetation (29.8 ± 10.0 mg CH₄–C m⁻² day⁻¹). Diffusive CH₄ flux also showed marked seasonality, with divergent seasonal patterns among ecosystems. Forested vegetation and mixed palm swamp showed significantly higher dry season (47.2 ± 5.4 mg CH₄–C m⁻² day⁻¹ and 85.5 ± 26.4 mg CH₄–C m⁻² day⁻¹, respectively) compared to wet season emissions (6.8 ± 1.0 mg CH₄–C m⁻² day⁻¹ and 5.2 ± 2.7 mg CH₄–C m⁻² day⁻¹, respectively). In contrast, forested (short pole) vegetation and M. flexuosa palm swamp showed the opposite trend, with dry season flux of 9.6 ± 2.6 and 25.5 ± 2.9 mg CH₄–C m⁻² day⁻¹, respectively, versus wet season flux of 103.4 ± 13.6 and 53.4 ± 9.8 mg CH₄–C m⁻² day⁻¹, respectively. These divergent seasonal trends may be linked to very high water tables (> 1 m) in forested vegetation and mixed palm swamp during the wet season, which may have constrained CH₄ transport across the soil–atmosphere interface. Diffusive N₂O flux was very low (0.70 ± 0.34 µg N₂O–N m⁻² day⁻¹) and did not vary significantly among ecosystems or between seasons. We conclude that peatlands in the PMFB are large and regionally significant sources of atmospheric CH₄ that need to be better accounted for in regional emissions inventories. In contrast, N₂O flux was negligible, suggesting that this region does not make a significant contribution to regional atmospheric budgets of N₂O. The divergent seasonal pattern in CH₄ flux among vegetation types challenges our underlying assumptions of the controls on CH₄ flux in tropical peatlands and emphasizes the need for more process-based measurements during periods of high water table.