A highly anionic peroxidase was strongly suggested to be involved in the deposition of the aromatic domain of suberin. cDNA containing the coding region of the suberization-associated anionic peroxidase from potato has been cloned and sequenced. The deduced amino acid sequence of the peroxidase shows that it is an anionic protein with considerable homology to other peroxidases. The amino acid sequence of two tryptic peptides obtained from the anionic peroxidase purified from suberizing potato tuber slices matched exactly with two segments of the amino acid sequence deduced from the nucleotide sequence of the cloned cDNA. The identity of the cloned cDNA is further supported by hybrid-selected translation and immunological recovery of the product with antibodies prepared against the purified anionic peroxidase. This anionic peroxidase was barely detectable at 2 days after wounding, and reached a maximal level at 8 days after wounding. Using the cDNA for the anionic peroxidase as a probe, we showed that the mRNA for the enzyme was induced in suberizing potato. The mRNA levels increased from an undetectable level in control tuber tissue to a maximal level in suberizing tuber tissue aged for four days. In suberizing tomato fruit the peroxidase mRNA showed induction and the level reached a maximum in three days. Ine data suggest that the induction of the peroxidase by wounding is preceded by transcriptional activation of the peroxidase gene or by increased stabilization of the mRNA. The time course of increase in mRNA for the anionic peroxidase was consistent with its postulated role in suberization.