The end-Permian mass extinction, the greatest biotic crisis through the Phanerozoic, caused a severe loss of marine organisms in terms of abundance and diversity. Knowing sea level fluctuations, environmental conditions and the sequence stratigraphic architecture of the Upper Permian deposits will enable us to reconstruct events before the mass extinction and across the Permian/Triassic boundary in a regional and global context. The Upper Permian deposits are examined in well-known sections in Julfa, NW Iran and Abadeh in SW Iran using microfacies analyses, depositional environment interpretation and sequence stratigraphic framework. Detailed petrographic examination and microfacies analyses show third- and fourth-order cycles both in Wuchiapingian and Changhsingian deep-water distally deposited strata of Julfa and Abadeh sections. Considering Iranian tectonics during Permian through Triassic time, there was rifting accompanied by drift and subsequent subsidence. Tectonics was a main factor that influenced the depositional environment and sequence stratigraphic framework in the study areas. According to previous studies, since subsidence increased in a North to SW direction during Middle Permian through Triassic time, this effect is seen in lithologic characteristics of the Wuchiapingian with more mid-ramp settings in Julfa Beds in Julfa area, compared to the more outer-ramp settings of the Unit 6 of the Hambast Formation in Abadeh area. Tectonic subsidence influence was also responsible for creating the fourth-order cycles within third-order cycles despite the absence of common glacial events to create high-frequency cycles in Iran during the Lopingian. The Lopingian successive deepening in Iran caused the faunal changes which is evident in decreasing trend of body size and biodiversity in brachiopods and ammonoids and also marks the beginning of the transgressive system tracts during this time interval.