Seagrass beds support high productivity and biodiversity of associated animal communities. Catastrophic disturbances, such as by tsunamis, are expected to affect not only abundance and diversity of seagrass, but also those of benthic animals inhabiting seagrass beds. To examine tsunami effects on infaunal seagrass communities, we compared several seagrass beds that had received various levels of impact from the tsunami that hit the Andaman Sea Coast of Thailand. Infauna were collected in 2001 (before the tsunami) and in 2005 (after the tsunami) within seagrass vegetation and in areas with no vegetation. Polychaetes were the most abundance taxa, followed by crustaceans. Density increased over time in some seagrass vegetated areas, whereas it deceased in non-vegetated areas, suggesting that the tsunami impacts varied with and without seagrass vegetation. Multivariate analysis on the polychaete assemblage revealed that temporal changes in assemblage structure occurred in different direction between vegetated and non-vegetated areas, and that the degree of temporal changes was not necessarily related to the magnitude of the tsunami disturbance.