Seagrass landscape structure provides habitat complexity, shelter and food availability for macrofaunal benthic animals. This study investigated the effect of spatial structure of seagrass landscape and its temporal dynamics on macrofauna community. Macrofaunal assemblages were collected from Zostera marina beds, Z. japonica beds and unvegetated area in 2006. The exact location of each sampling point was plotted on GIS maps showing annual changes in landscape structure during 2002-2007. Based on GIS analyses, we estimated coverage of seagrass at different spatial scales (1-50 m extents), and the stability of vegetation at each point. Density and species diversity of macrofauna were significantly greater in Z. marina beds than in Z. japonica beds and unvegetated area. Effect of vegetation was greatest when we observed the seagrass coverage at extents of 10-15 m. Macrofaunal abundance and diversity were significantly lower at sites where seagrass vegetation was unstable. Our findings indicate that the seagrass landscape structure greatly affects macrofaunal assemblages.