Epiphytic microalgae attached to Posidonia oceanica leaves play a significant role through primary production, nutrient cycling and trophic fluxes in benthic ecosystems. Due to their sensitivity, epiphytic microalgae respond to environmental alterations more quickly than their host. The aim of this study is therefore to evaluate the ecological quality in Gokceada Underwater Park (North Aegean) using epiphytic microalgal composition and abundance. In this respect, P. oceanica shoots are collected at 6 m, 15 m and 28 m in May, July, October 2009 and January 2010 to estimate the microalgal composition and abundance. Also, P. oceanica descriptors and physico-chemical parameters in the water column of the meadow lower limit are measured. Leaf surface improvement through greater depths, have provided a convenient substratum for epiphytic colonization. A total of 56 taxa belonging to epiphytic microalgae are composed of Bacillariophyceae (91%), Cyanophyceae (7%) and Dinophyceae (2%). Temporal and bathymetric dynamics of the epiphytic community structure and abundance depend on the environmental parameters; such as leaf surface, nutrients and turbidity. Also, a mucilage phenomenon, resulted in a low diversity due to the dominancy of filamentous cyanobacteria. Necessary data is supplied for a less evaluated region affected by agricultural activities and urbanization in the recent years.