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Dolomite [CaMg(CO3)2] is used widely for soybean, Glycine max (L.) Merr. production in Japan to amend soil pH, although magnesium (Mg) in the dolomite can inhibit soybean growth and yield. The aim of this study was to determine the effect of Mg on soybean production in a paddy – upland rotation field in 2019–2020 by comparing the application of dolomite and calcite (CaCO3). The field test included three replications with three lime applications: control (no lime), dolomite, and calcite. The amounts of calcite and dolomite applied in each year were 253 and 259 g m−2, respectively. The soil pH was almost similar following the applications of calcite and dolomite, whereas the soil exchangeable Mg content was higher following the dolomite application than following the other applications. The shoot weight from the flowering stage to the harvest stage (R8) was significantly higher following the calcite application than following the other applications. However, the shoot weight at only R8 was significantly higher following the dolomite application than following the control application. In 2019–2020, the highest soybean yield was resulted from the calcite application (355 g m−2) followed by the dolomite application (312 g m−2) and the control application (260 g m−2). The severity of soil-borne diseases was lower following the dolomite application than following the control application, and even lower following the calcite application. Thus, the application of dolomite increased soybean yield by improving soil pH; however, Mg in the dolomite inhibited a further increase in soybean yield in a paddy – upland rotation field.