Heavy metal contamination resulting from anthropogenic activities is one of the major environmental problems in the modern world. Progress toward creating modified plants that are more efficient in phytoremediation requires an understanding of the anatomical and ultrastructural changes involved in heavy metal accumulation. A large supply of zinc (Zn) is toxic for plants and can lead to functional and structural disorders. The present study investigates the anatomical and ultrastructural responses of Brassica napus (rapeseed) to excess Zn after long-term exposure. Results showed that Zn bioaccumulation in the roots and leaves of plants treated with 350 μM Zn2+ was severely increased, leading to a variety of anatomical and ultrastructural alterations in several cell types. Overall, although B. napus has been reported as a metal-accumulator species, our data revealed that B. napus cultivar Hayola 401 could not tolerate a high concentration of Zn and thus is not a good candidate for Zn phytoremediation.