The horizons in soil profile will determine the magnitude of greenhouse gas production due to the difference of total organic carbon and other chemical properties. This study aimed to determine the potential production of methane (CH<sub>4</sub>) and nitrous oxide (N<sub>2</sub>O) in each horizon of soil profile from organic and conventional rice fields. Soil samples which were taken from Imogiri Bantul D.I. Yogyakarta were used to determine soil properties, the potential of CH<sub>4</sub>, and N<sub>2</sub>O productions. The correlation analysis was used to determine the relationship between the production of CH<sub>4</sub> and N<sub>2</sub>O with soil properties. The results showed that production of CH<sub>4</sub> and N<sub>2</sub>O will be decreased with the increase of soil depth. Production of CH<sub>4</sub> and N<sub>2</sub>O was higher in organic rice field than in conventional rice field. The total organic carbon (TOC) correlated positively with CH<sub>4</sub>-production (<em>r=0</em><em>.89, P&lt;0.001, n=8</em>) and N<sub>2</sub>O-production (<em>r=0</em><em>.87, P&lt;0.001, n=8</em>). The nitrogen content also correlated positively with CH<sub>4</sub>-production (<em>r=0</em><em>.87, P&lt;0.001, n=8</em>) and N<sub>2</sub>O-production (r=0.94, P&lt;0.001, n=8). Mitigation of CH<sub>4</sub> and N<sub>2</sub>O emissions should consider of C and N in the soil.