The transcription factor encoded by PAX3 is among the first expressed in the embryo, with a key role in development of the melanocytic lineage. Re-expression of PAX3, consistently observed in cutaneous malignant melanoma (CMM) as compared to normal melanocytes, appears linked to progression of CMM. Previous research has identified PAX3d (encoded by exons 1-9) as the predominant isoform present in CMM, together the with an alternate isoform PAX3c (encoded by exons 1-8). We investigated the expression of Pax3c and Pax3d transcripts during mouse development. The reverse transcription-polymerase chain reaction and immunohistochemistry experiments presented here implicate these transcripts in melanoblast development and demonstrate significant spatial and temporal differences in their expression. Differences in expression were also noted during active hair regrowth in adult skin, which is accompanied by proliferation and migration of melanoblasts into the hair cortex to color new hair. Results indicate that the defined spatial and temporal expression of Pax3d may be linked to either melanoblast proliferation or migration during melanogenesis.