The present study describes the structure and seasonal distribution of polychaete assemblages inhabiting seagrass beds of Halphila stipulacea species in Abo Monkar Island coast, Red Sea, near Hurghada city, during the period from mid-April 2016 to mid-January 2017. Seasonal samples of seagrass canopies and roots from the edge and center of 3 different sized seagrass patches were examined for their polychaetes content to figure out the effect of different habitat variables on the abundance and diversity of polychaetes. Such variables comprise habitat fragmentation, edge effects and microhabitat nature beside the effect temporal variation.  
Overall, 35 polychaete species belong to 18 families were recorded, from all different seagrass patches with a comparable temporal distribution in 2 main marked seagrass habitat categories involving the canopy and root.  Results indicated that large seagrass patches harbor higher polychaete's abundance than medium and small seagrass patches in seagrass canopies microhabitat especially in warm seasons, which promote the assumption of the negative effect of seagrass fragmentation, which become positively correlated with the increasing of water temperature and become more noticeable in the summer season. Reduction of habitat size led to reducing the polychaetes species richness in both seagrass canopies and roots. Total polychaetes abundance is relatively increased toward the patch's edge with the increasing of temperature whereas such animals tend to colonize patch's center in the winter season (in seagrass canopy microhabitat) as well as root microhabitats. However, polychaetes species richness was markedly increased in the patch-edge habitat only in seagrass canopies in only large continuous patch summer and spring seasons recording 19 and 20 species respectively. Our findings suggested that polychaete species tend to migrate toward the patch center or seagrass roots microhabitats whenever temperature and vegetation cover is reduced.