The order Saprolegniales includes pathogenic species of aquatic and terrestrial plants and aquatic animals including fish. These Straminipilous fungi play an important role as a decomposing component which participates in the destruction processes of organic substrates and self-cleaning biological processes in freshwater ecosystems. In this study, in order to isolation and identification of these Straminipilous fungi, samples of brown decayed twigs, leaves and woods from various places of Fars and Kermanshah Provinces, Iran (Sepidan, Dalkhan, Bahreghan, Tang-e-Sorkh, Sheshpir, Sahneh, Harsin, Bisotun and Paveh) were transferred to the laboratory during the fall and winter 2017. The samples were rinsed in distilled water, cut off into segments, were placed in sterilized water in Petri dishes containing several halves of hemp seeds (Cannabis sativa), and incubated at room temperature (15-20 °C). After 7- 14 days, the colonized hemp seed baits, were rinsed in distilled water then transferred to Cornmeal Agar medium. Purification of isolates was carried out using a Water-Agar culture medium and conducting hyphal-tip. Primary identification was carried out using: A Manual of Aquatic Fungi (Khulbe 2001). Species were identified based on morphological and morphometric characteristics of sexual and asexual organs as well as the physiological and phylogenetic studies. Identified species were sequenced based on the internal transcribed spacer (ITS) region of rDNA and were analyzed phylogenetically by Maximum Likelihood method. Six species of Saprolegnia and one species of Achlya were identified including: Saprolegnia parasitica, S. frax, S. anomalies, S. australis, S. mixta, Saprolegnia sp. and Achlya americana. Saprolegnia anomalies, S. australis, S. mixta Saprolegnia sp. and Achlya americana were new to Iran mycobiota.