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The main diatomic structure-forming species of the Zayandehrud Reservoir was investigated by collecting samples from the surface, five, seven and 10 m depths from January 2011 to October 2012 along four linear transects. Asterionella formosa Hassall, Cyclotella ocellata Pantocsek and Fragilaria crotonensis Kitton were revealed as the three structure-forming species among diatomic algae in the reservoir. The number of these diatomic cells increased from the reservoir banks to its central areas, but their abundance was non-uniformly distributed at the 10-meter water column at different sites, except for C. ocellata that showed a practically uniform distribution at the peak of its maximum growth. Overall, the frequency and cover of these structure-forming diatoms changed under the influence of different abiotic variables such as electrical conductivity (EC) and nitrate (NO₃-N).