The 3.6 Ma El'gygytgyn structure, located in northeastern Russia on the Chukotka Peninsula, is an 18 km diameter complex impact structure. The bedrock is formed by mostly high‐silica volcanic rocks of the ~87 Ma old Okhotsk‐Chukotka Volcanic Belt (OCVB). Volcanic target rocks and impact glasses collected on the surface, as well as drill core samples of bedrock and impact breccias have been investigated by thermal ionization mass spectrometry (TIMS) to obtain new insights into the relationships between these lithologies in terms of Nd and Sr isotope systematics. Major and trace element data for impact glasses are added to compare with the composition of target rocks and drill core samples. Sr isotope data are useful tracers of alteration processes and Nd isotopes reveal characteristics of the magmatic sources of the target rocks, impact breccias, and impact glasses. There are three types of target rocks mapped on the surface: mafic volcanics, dacitic tuff and lava of the Koekvun’ Formation, and dacitic to rhyolitic ignimbrite of the Pykarvaam Formation. The latter represents the main contributor to the impact rocks. The drill core is divided into a suevite and a bedrock section by the Sr isotope data, for which different postimpact alteration regimes have been detected. Impact glasses from the present‐day surface did not suffer postimpact hydrothermal alteration and their data indicate a coherent alteration trend in terms of Sr isotopes with the target rocks from the surface. Surprisingly, the target rocks do not show isotopic coherence with the Central Chukotka segment of the OCVB or with the Berlozhya magmatic assemblage (BMA), a late Jurassic felsic volcanic suite that crops out in the eastern part of the central Chukotka segment of the OCVB. However, concordance for these rocks exists with the Okhotsk segment of the OCVB. This finding argues for variable source magmas having contributed to the build‐up of the OCVB.