Gene segments encoding the 70 and 22-kDa peroxisomal membrane proteins (PMP) have been characterized in mice and compared with other peroxisomal proteins in terms of evolution and expression. The mouse PMP22 gene sequence predicts A16G and I136V substitutions that agree with those defined by cyanogen bromide cleavage analysis, providing additional evidence that this gene encodes the major 22-kDa membrane protein visualized by SDS-polyacrylamide electrophoresis. Mammalian PMP22 genes exhibit high evolutionary rates (0.17% amino acid substitution per million years) than PMP35 (0.14%), PMP70 (0.07%), or catalase genes (0.13%). PMP70 gene regions are conserved throughout vertebrate phylas based on Southern analysis, while PMP22 sequences were only detected in rodents. Amino acid substitutions are clustered in both PMP22 and PMP70 genes, and their pattern supports membrane topologies derived from hydropathy profiles. Northern blot analysis identifies single mRNAs of 4.6 kb (PMP70), 1.4 kb (PMP22), and 2.3 kb (catalase) in several rodent tissues. Quantitative or competitive RT-PCR assays detected two- to three-fold greater numbers of catalase mRNA molecules relative to PMP mRNA molecules in brain, liver, and kidney; PMP22 and PMP35 mRNAs were two-fold more abundant than PMP70 mRNA in these tissues. Steady-state levels of PMP22 mRNA were highest in rodent liver kidney, spinal cord, and duodenum with low levels in colon, adrenal, thymus, and spleen. We conclude that PMP genes exhibit independent evolutionary rates and tissue regulation, suggesting that they have unique roles in peroxisome biogenesis and tissue differentiation.