Several studies have reported differences in physiological and pathological phenotypes between different strains of experimental mice, such as environment-based behavior, skin damage, damage in response to toxins and nervous system injury. However, the mechanisms underlying these differences have not yet been fully elucidated. We have been studying the function of kallikrein-related peptidases (KLKs), serine proteases known to serve a variety of functions. In this study, we focused on differences in KLKs between C57BL/6 mice and 129 mice. Among 13 KLKs genes examined, 12 KLKs showed differences in the mRNA coding region sequence and 7 KLKs showed different deduced amino acid sequences of their proteins when comparing C57BL/6 and 129 mice. KLK6 protein from 129 mice had six amino acid differences compared with that from C57BL/6 mice. KLK6 protein from 129 mice showed reduced SDS-PAGE mobility compared with that from C57BL/6 mice. Moreover, recombinant KLK6 protein from 129 mice had a higher optimum pH and >15 times higher hydrolytic enzymatic activity for several substrates than that from C57BL/6 mice. These results suggest that KLKs may contribute to the genetic basis of the differences between mouse strains.