Periphyton is an essential part of aquatic ecosystems that can remove toxic substances, nutrients and metals from water, and therefore it can be considered as one of the important options in ecotoxicological studies. The aim of this study was to identify the autotrophic periphytic components (APC) in some Iranian aquatic ecosystems and investigate the possibility of its re-culture under in-vitro condition. Limnological (chemical and biological) properties of bed sediments, periphytic biofilms, and water of lakes, such as biological and chemical oxygen demand (BOD and COD), pH, EC, temperature, nitrogen, total and available phosphorous were measured. Then APC of Epixylon and lakes water samples were isolated and purified in their specific culture medium. Based on results, identified genera included a variety of filamentous and single-celled algae, cyanobacteria, and diatoms. In Fashtam Lake, Chlorophyceae, Charophyceae, Euglenozoa, Ochrophyta, Bacillariophyceae, and Cyanobacteria constituted about 38.48%, 20.58%, 1.72%, 1.74%, 19.68%, and 19.52% of the APC, respectively. In Tazesel Lake, Chlorophyceae, Euglenozoa, Bacillariophyceae, and Cyanobacteria constituted about 13.93%, 0.56%, 51.9%, and 33.6%, and in Qalewersel Lake, Chlorophyceae, Bacillariophyceae, and Cyanobacteria constituted 26.24%, 56.06% and, 17.69%, respectively. To in-vitro re-culture of periphyton, all purified genera from each lake were mixed and introduced to medium, in the presence and absence of substrate and maintained in growth chamber (appropriate conditions) for 30 days. After incubation period, different genera of Chlorophyceae, Cyanobacteria and Bacillariophyceae were accounted for 70%, 20%, and 10% of the re-cultured APC in Fashtam Lake, 51.6%, 33.3%, and 15%, in Tazesel Lake, and 59.33%, 28.33%, and 12.33% in Qalewersel Lake, respectively. As a general result, it can be stated that the frequency of filamentous species of APC re-cultured on the carrier is higher than that of single-celled species of APC in greenhouse condition. Also, in this research, a great similarity was observed between the APC isolated from periphyton in the autumn season with the APC isolated and identified from re-cultured periphyton in the greenhouse; so that the predominant APC was related to the cyanobacteria, chlorophyta and bacillariophyta. [GRAPHICS] .