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In order to estimate S-wave velocity structure of the thick sedimentary structure in the Nagaoka Plain, SPAC (spatial autocorrelation) method was used for data analysis. 17 seismic observation data (one-hour continuous records) were selected and disperse curves of Rayleigh waves were calculated by SPAC method, from which the S-wave velocity structure was estimated using genetic algorithm (GA). The results showed that the depth of the seismic basement (Vs >= 3.0 km/s) was about 4 ~ 6 km and the depth at which Vs becomes ~4.0 km/s was about 10.6 ~ 12.5km in the Nagaoka Plain.