From investigation of 2000 soil isolates, we identified a D-stereospecific metallo-amidohydrolase that can hydrolyze D-aminoacyl derivatives from the culture supernatant of Bacillus sp. 62E11: 62E11DppA. The enzyme binds two equivalents of zinc, exhibits 70% identity with that of D-aminopeptidases from Bacillus subtilis (DppA). In fact, 62E11DppA has strict specificity toward D-aminoacyl derivatives, i.e., the enzyme shows high activity toward D-aminoacyl benzyl esters and little activity toward D-amino acid containing peptides. Moreover, 62E11DppA exhibits a dramatic change in its activity and substrate specificity by substitution of metal ions in its active site. Based on results of kinetic studies using apo-62E11DppA with various metal ion and substrate concentrations, we propose a possible mechanism for the change in its activity and specificity by substitution of metal ions: the substitution of metal ions in 62E11DppA dramatically changes its activity by altering the substrate specificity.