Tajan River is one of the significant rivers of Caspian Sea which is originated in Alborz mountains and This study was carried out in Tajan river from March 2007 to February 2008. Samples were taken from amongst stones in monthly interval periods. Samples were immediately fixed with formaldehyde 4% insitu. For exact recognition, permanent mounts were prepared by using Patrick & Reimer procedure. Identification of diatoms was done by means of light microscope and specialized recognition keys. For study of diatom communities in aquatic ecosystems, counting method is used because in this method, identification and determination of diatom communities and morphological variations of species are better known. Water temperature, pH, EC, DO, TDS, BOD, COD, PO43-, NO3-, SiO2, Na+, Ca2+, SO42-, K+, Mg2+, Clˉ and Nh4+ were analysed during the study. In this research 95 species and 23 genera of epilithic diatoms were identified. Epilithic diatoms have been recommended by researchers from several countries as particullary suitable for water quality evaluation. Multivariate analyses of species composition data were applied in two different approaches. Firstly, species and sampling stations were grouped using TWINSPAN (Two Way Indicator Species Analysis). Secondly, Canonical Correspondence Analysis (CCA) was applied in order to uncover the main gradients of changes in species composition relating this change to the pollution.