––Information on the distribution of earthquake hypocenters for many seismically active zones of Siberia remains insufficient, which is associated with sparse networks of seismological observations. The paper presents the results of determining the earthquake depths in several seismogenic areas in the Altai-Sayan region, Cisbaikalia, Transbaikalia, and Yakutia using the travel time of longitudinal refracted waves from the Mohorovičič discontinuity (Pn waves) from earthquakes and the recently obtained information about the deep structure of these regions. The depth determination algorithm is tested using data from aftershocks of large earthquakes occurring in Tuva in 2011 and 2012 (ML = 6.7 and 6.8), recorded both by the regional seismological network and by a local group of seismic stations. Different methods are applied to reveal that some aftershock depths have a close match, including those for the main shocks – the Tuva-1 and Tuva-2 earthquakes. Another good match of earthquake depths is obtained using Рn waves with materials from regional and detailed studies of the Baikal branch of the Geophysical Survey of the Russian Academy of Sciences in the Muyakan activation site in the Baikal rift zone. The resulting data complement the information on the hypocenter of the main shock and confirm the change of the Muyakan activation cluster from large depths to shallow ones since the onset of activation in 2014. New information on the earthquake depths using Рn waves is obtained in Yakutia along the border of the largest Eurasian and Okhotsk tectonic plates. It is revealed that they decrease to 6–12 km as compared to higher depths of 20–30 km in adjacent areas. The resulting series of new information on the distribution of earthquake hypocenters using Рn waves is extremely important mostly because it indicates the possibility of identifying and redefining earthquake hypocenters using previous seismological observations in seismically active zones of Siberia.