This study was conducted to determine the inheritance of anthocyanin production and of malate dehydrogenase banding patterns in Agastache rugosa. Results of the study support the hypothesis that anthocyanin production is controlled by a single dominant gene, designated as A, for anthocyanin production. The Mdh-3 banding patterns are controlled by two alleles, each of which associated with a two-banded phenotype. A monomeric quaternary structure of MDH, which is rather atypical among plant species, can be inferred from the results. No linkage was found between the loci governing anthocyanin production and Mdh-3 banding patterns. This is the first report of heritable variability in A. rugosa.