Structural complexity of seagrass bed including species composition and shoot density is argued to be an important factor determining fish assemblages. However statistical verification of such a relationship is possible only in areas with high species richness of seagrass and fish assemblages which is observed in tropical waters. Material for this study was collected in three seagrass beds with different structure in Inner Ambon Bay, Eastern Indonesia. This study provided evidence that higher structural complexity of seagrass bed was related to the higher richness, abundance, and biomass of fish. However, lower structural complexity of seagrass patch should not be underestimated because it provided different habitat for various stages of life in fish. Smaller fish preferred to occupy dense seagrass of dominant pioneer small-sized species ( Halodule uninervis ) and moved to the lesser dense bed of climax large-sized seagrass ( Thalassia hemprichii and Enhalus acoroides ) with increasing their size. This finding is important for seagrass-fisheries management.