Carbon dioxide emission through soil respiration is an important component of the carbon balance in forest ecosystems. However, little information is available on the rates of soil respiration in mangrove forests. We studied the rate of soil respiration in a secondary mangrove forest in eastern Thailand on an estuary of the Trat River during both the wet and dry seasons. A study site of 40 × 110 m was established and a series of vegetation zones identified: Sonneratia, Avicennia, Rhizophora and Xylocarpus, in order of increasing elevation inland. Soil respiration was measured during low tide, using an infrared gas analyser connected to a respiratory chamber, by excluding the respiration of above-ground roots from the chamber. At least 19 measurements were performed in each zone for each season. The rate of soil respiration significantly increased with increasing soil temperature. The soil temperature which was usually lower than that of sea water showed a trend that decreased with distance from the river in both wet and dry seasons. The relative land elevation causes different periods of inundation among the vegetation zones. The period was longest in the Sonneratia zone located on the river fringe, and became shorter moving inland. Thus, the elevation and relevant period of inundation are considered to be causal factors warming the soil. Consequently, the difference in soil temperature caused significantly different rates of soil respiration among the vegetation zones in the mangrove forest. Overall, the average rate of soil respiration ranged from 0.456 to 0.876 μmol CO2 m−2 s−1, supporting the view that mangrove forests have lower rates of soil respiration than do upland forests.