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To understand mechanisms of generation of abnormally high PGA during the Tohoku earthquake, soil behavior in the near-fault zones is studied. Based on vertical array records, models of soil behavior, i.e., vertical distributions of stresses and strains induced in soil layers changing with time during strong ground motion are constructed. The models indicate “atypical” soil behavior: instead of reduction of shear moduli in soil layers during strong ground motion, at soft and dense soil sites recorded the highest PGA shear moduli increased and reached their maxima at the moments of the highest intensity of motion, indicating soil hardening, then reduced. No strong or widespread nonlinearity of soft soil behavior was observed. Evidently, soil hardening and weak nonlinearity contributed to the occurrence of abnormally high PGA during the Tohoku earthquake. We can assume that, while during previously studied smaller earthquakes with Mw~7.0 soils were subjected to rather short loadings of impulse (usually) type and behaved nonlinearly (softened), during the Tohoku earthquake, soils experienced long-duration (~3 minutes) dynamic loadings of variable (or slowly increasing) intensity. In response to such loadings, soft and dense soils consolidated and compacted, and abnormally high PGA resulted from the amplification of the pulse bursts by pre-consolidated soils. On the other hand, some facts testify to the occurrence of a shock wave during crack propagation in the source of the Tohoku earthquake, which resulted in soil compression and constructive interference of seismic waves at sites recorded the highest PGA. Evidently, such soil behavior with their compaction and generation of high PGA can be expected during future mega-thrust earthquakes.