The sequences of cDNA clones encoding the Bowman-Birk proteinase inhibitor (BBPI) and its isoinhibitors (D-II and C-II) have been identified. Nucleotide sequence homologies among these clones and between the two reactive domains in each clone were very high. These homologies suggest that the BBPI and its isoinhibitor genes may have evolved from a common ancestral inhibitor. Also, clone pB2 (D-II) had two identical reactive sites that inhibit trypsin only, and three repetitive regions that are about 81 bp and initiated with ATG. It was assumed from these results that isoinhibitor D-II was the most primordial type of these inhibitors.