The myelin basic protein (MBP) gene is a complex gene which codes for several distinct forms of MBP. The various forms of MBP are functionally involved in the development of the nervous system, T-cell regulation, and myelination. Several neurological disorders have been linked to MBP abnormality, further demonstrating its functional significance in the nervous system. The white-footed mouse (Peromyscus leucopus) exhibits profound neuroprotective characteristics, is asymptomatic to various disease-states, and has a lifespan twice that of the house mouse (Mus musculus). We used M. musculus mouse MBP as a reference to explore MBP in P. leucopus mice. Through genetic and downstream proteomic data analysis, we identified a novel variant of the BG21 isoform of MBP in P. leucopus mice. Variation in this isoform is present at the genetic level between the two species of mice. Our results show differences within the open reading frame of the transcripts accompanied by corresponding differences in protein structure prediction. These data introduce the potential of MBP variation as one of many causal variables contributing to the unique presentation of enhanced neuroprotection and longevity in P. leucopus mice.