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Histone acetylation plays an important role in plant growth and development. Here, we investigated the effect of sodium butyrate (NaB), a histone deacetylase inhibitor, on adventitious shoot formation from protoplast-derived calli and cotyledon explants of tobacco (<i>Nicotiana benthamiana</i>) and tomato (<i>Solanum lycopersicum</i>). The frequency of adventitious shoot formation from protoplast-derived calli was higher in shoot induction medium (SIM) containing NaB than in the control. However, the frequency of adventitious shoot formation from cotyledon explants of tobacco under the 0.1 mM NaB treatment was similar to that in the control, but it decreased with increasing NaB concentration. Unlike in tobacco, NaB decreased adventitious shoot formation in tomato explants in a concentration-dependent manner, but it did not have any effect on adventitious shoot formation in calli. NaB inhibited or delayed the expression of D-type cyclin (<i>CYCD3-1</i>) and shoot-regeneration regulatory gene <i>WUSCHEL</i> (<i>WUS</i>) in cotyledon explants of tobacco and tomato. However, compared to that in control SIM, the expression of <i>WUS</i> was promoted more rapidly in tobacco calli cultured in NaB-containing SIM, but the expression of <i>CYCD3-1</i> was inhibited. In conclusion, the effect of NaB on adventitious shoot formation and expression of <i>CYCD3-1</i> and <i>WUS</i> genes depended on the plant species and whether the effects were tested on explants or protoplast-derived calli.