—The Malyi Orgochor, Orgochor, Birbash, Sukhoi Ridge, Ichketosma, and Tosma uplifts in the eastern Issyk-Kul basin are fault-related anticlinal folds composed of Neogene and Quaternary sediments involved in tectonic movements. The folds have asymmetric transversal profiles, with low-angle southern limbs and steep northern limbs cut by segments of the South Issyk-Kul and Karkara reverse faults reactivated in the late Quaternary. The location and geometry of the two faults, which both show reverse and left-lateral strike slip components, correspond to neotectonic propagation of deformation from the Terskey-Ala-Too Range over almost the whole eastern Issyk-Kul basin. Judging by primary and secondary coseismic surface deformation in the area, the South Issyk-Kul and Karkara faults repeatedly generated large earthquakes (M ≥ 7, I ≥ 9) in the Late Pleistocene and Holocene. According to trenching results, the historical earthquakes that occurred in the first and 10–11th centuries accommodated motions on the South Issyk-Kul fault. The new seismotectonic and paleoseismicity data from the eastern Issyk-Kul basin provide updates to its seismic potential.