Total thyroxine was assessed by radioimmunoassay for 58 female deer mice of two subspecies (Peromyscus maniculatus bairdii and P. m. gracilis) and two color morphs (agouti and non-agouti). P. m. bairdii of both color-morphs had significantly higher mean thyroxine levels than P. m. gracilis. Non-agouti deer mice of both subspecies had significantly higher mean thyroxine levels than agouti deer mice. This is the first report of thyroid hormone differences associated with the non-agouti allele.