Convergent beam electron diffraction (CBED) performed on two-dimensional (2D) materials recently emerged as a powerful tool to study structural and stacking defects, adsorbates, atomic 3D displacements in the layers, and the interlayer distances. The formation of the interference patterns in individual CBED spots of 2D crystals can be considered as a hologram, thus the CBED patterns can be directly reconstructed by conventional reconstruction methods adapted from holography. In this study, we review recent results applying CBED to 2D crystals and their heterostructures: holographic CBED on bilayers with the reconstruction of defects and the determination of interlayer distance, CBED on 2D crystal monolayers to reveal adsorbates, and CBED on multilayered van der Waals systems with moiré patterns for local structural determination.