Summary: A marker assisted selection protocol is presented that allows for the generation of congenic or consomic strains derived from a C57BL/6J:129S6/SvEvTac mixed strain background. The protocol uses defined primer pairs to generate amplicons that can be distinguished by non-denaturing agarose electrophoresis. Use of this application should result in substantial savings in time, effort, and cost for investigators in all areas of transgenic mouse research.