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New results of detailed study of deep‐seated structure are presented for the Podvodnikov Basin. Interpretation of seismic lines in network over the East Siberian Sea is accepted to be a work basis. Two main stages of seismic complex formation—synrifting and postrifting—are distinguished in section of sedimentary cover. One phase of synrifting, whose boundary is traced at Aptian–Albian, has been established. The unconformity dated at Cretaceous–Paleogene in the East Siberian Basin is caused by two factors: completion of synrifting and superposition of deformations related to strike‐ slip shearing and compression. The Podvodnikov Basin was formed in Aptian–Albian, being related to coeval onset of rifting, which is dated close to age of basalts from De Long plateau. An age of rifting–post‐rifting is dated conditionally, as a boundary between Early and Late Cretaceous. Since the Late Cretaceous, the Podvodnikov Basin has gradually undergone a thermal post‐rifting submergence. Clinoforms have been identified in postrifting sedimentary cover. The history of their formation may be preliminarily divided into three stages: (i) Paleocene–Eocene, whose sole serves as boundaries of (ii) Cretaceous– Paleogene unconformity; (iii) Eocene–Pliocene or Pliocene–Quaternary. A strongly extended and flattened continental crust is suggested for the Podvodnikov Basin. This is followed from typical rift structures at the base of section. Rifts with such geometry and synrift sediments are typical for continental rifting.