The taxonomical composition of epipelic diatoms was investigated at four stations in Homa Lagoon during June 2006 and September 2007. A total of 54 diatom taxa were determined and dominated by pennate diatoms. Cocconeis scutellum, Eunotogramma marinum, Mastogloia lanceoalata, Navicula abrupta, N. cincta, N. cryptocephala var. veneta, N. cryptotenella, Nitzschia apiculata, Psammodictyon panduriforme, Rhabdonema adriaticum and Stauroneis amphioxys were found at all stations. The collected seasonal samples at each station constituted seven seperate groups in the MDS plot, which were correlated with a combination of environmental variables such as temperature, the concentrations of nitrite and percentage of total organic carbon in the sediment (rho r=0.15).