The first step for development of a functionally and structurally intricate organ, the brain, involves precise control of the neural stem cell (NSC) fate. NSCs produce a variety of neurons and glial cells according to the developmental time and 3-dimensional (3D) position within the brain. Morphogens play a key role in determining the 3D positional information of NSCs and thus regulating brain arealization along the rostrocaudal and dorsoventral axes. In this review article, we summarize recent studies that described essential roles of Polycomb group proteins in the establishment of the 3D atlas of the brain, in part through suppressing brain area-specific genes such as morphogens.