The Sayan and Tunka faults are located at the boundary between the northernmost mountain belt of Central Asia (the Sayan-Baikal ranges) and the Siberian platform. These prominent crustal structures were involved in the opening of the southern Baikal rift system since the beginning of the Cenozoic and define large-scale sharp morphotectonic features. Despite low instrumental seismic activity, Late Pleistocene-Holocene morphotectonic features along the two faults indicate that the faults are active and have the capacity to produce strong earthquakes. A careful mapping of the most recent trace of activity, within the southeastern parts of the two faults where they merge within a relay zone, demonstrates that they correspond now to left-lateral-reverse faults, suggesting a recent inversion of their vertical component. We also show that the two faults are now structurally connected via a young surface rupture and that no obvious post-Last Glacial Maximum ruptures are observed along the central part of the Sayan Fault beyond its junction zone with the Tunka fault. This suggests that the left-lateral strike-slip deformation is transferred from the eastern Sayan fault to the Tunka fault. A detailed morphotectonic study along the southeastern Sayan fault allows estimating a left-lateral slip rate between 1.3 (min) and 3.9 mm/year (max). Finally, a critical review of Russian paleoseismic data, combined with our paleoseismological investigations, allows us to propose that the mean recurrence time along the two faults is on the order of 4 kyr and that they may have either ruptured together or during seismic clusters.