The two isozymes of pancreatic amylase in mouse strain YBR/Ki are encoded by closely linked genes which are independently regulated. We have isolated these two pancreatic amylase genes, Amy-2.1 and Amy-2.2, from a cosmid library of YBR/Ki genomic DNA and compared the nucleotide sequences of coding regions with the amino acid sequences of the protein isozymes. Transcripts of both genes were also isolated from a pancreatic cDNA library and partially sequenced. The results demonstrate that Amy-2.1 encodes the A1 isozyme of YBR/Ki pancreatic amylase, while Amy- 2.2 encodes the insulin-dependent B1 isozyme. Similarities of restriction maps and nucleotide sequences suggest that Amy-2.1 is closely related to the active Amy-2a gene previously isolated from strain A/J (Schibler, U., Pittet, A.-C., Young, R. A., Hagenbüchle, O., Tosi, M., Gellman, S., and Wellauer, P. K. (1982) J. Mol. Biol. 155, 247-266). Expression of Amy-2.2 may be limited to strain YBR/Ki. The inactive Amy-X gene from A/J (Schibler, U., Pittet, A.-C., Young, R. A., Hagenbüchle, O., Tosi, M., Gellman, S., and Wellauer, P. K. (1982) J. Mol. Biol. 155, 247-266) is apparently a null allele of Amy-2.2. An additional amylase gene from YBR/Ki has been identified as a pancreatic amylase pseudogene which diverged between sixteen and thirty-two million years ago. The pancreatic amylase subfamily in strain YBR/Ki thus consists of two active genes and one pseudogene. The low rate of amylase production in YBR/Ki pancreas, relative to that of other inbred strains, can be accounted for by the lower number of gene copies in this strain. Comparison of pancreatic amylase genes from different inbred strains provides evidence for several duplication and deletion events during the recent evolution of this chromosome region.