A survey on the epiphytic microorganisms growing on Posidonia oceanica leaves was conducted along a depth transect along the coast of Eastern Tunisia (Mahdia). Samples were collected by SCUBA diving at depths of 3, 5, 10 and 12 m in July 2008 and January 2009. A total of 58 microepiphyte taxa were identified. Multivariate analyses revealed temporal and spatial variation of the abundance of epiphytic microalgae. Water motion, light availability, temperature and motility of species seem to be responsible of temporal and bathymetric variations of epiphytic microalgae. Unlike diatoms, dinoflagellates were more abundant in deep waters, suggesting that they are more vulnerable to hydrodynamics. The significant correlation between leaf area index and abundance of epiphytic species indicates that the phenological parameters of the host plant influence the abundance of the epiphytic microorganisms. Among the epiphytic dinoflagellates, our data showed a great number of potentially toxic species (Alexandrium minitum, Amphidinium carterae, Karenia selliformis, Coolia monatis, Karlodinium veneficum, Ostreopsis siamensis, Prorocentrum concavum, Prorocentrum minimum, Prorocentrum rathymum and Prorocentrum lima). These species were more abundant in the deep station under more sheltered conditions than found at inshore shallower stations, which are subjected to high water motion.