The Brain/MINDS 3D Digital Marmoset Brain Atlas Version 2.0 (BMA2.0) is a population-based, whole brain reference atlas for the common marmoset that overcomes the structural bias inherent to single subject atlases. It integrates a generalized cortical parcellation derived from ten manually delineated myelin-stained brains, refined subcortical annotations, and a newly constructed, detailed cerebellar parcellation.