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Layered transition metal dichalcogenides (TMDs) have attracted interest due to their promise for future electronic and optoelectronic technologies. As one approaches the two-dimensional (2D) limit, thickness and local topology can greatly influence the macroscopic properties of a material. To understand the unique behavior of TMDs it is therefore important to identify the number of atomic layers and their stacking in a sample. The goal of this work is to extract the thickness and stacking sequence of TMDs directly by matching experimentally recorded high-angle annular dark-field scanning transmission electron microscope images and convergent-beam electron diffraction (CBED) patterns to quantum mechanical, multislice scattering simulations. Advantageously, CBED approaches do not require a resolved lattice in real space and are capable of neglecting the thickness contribution of amorphous surface layers. Here we demonstrate the crystal thickness can be determined from CBED in exfoliated 1T-TaS2 and 2H-MoS2 to within a single layer for ultrathin ≲9 layers and ±1 atomic layer (or better) in thicker specimens while also revealing information about stacking order—even when the crystal structure is unresolved in real space.