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Ordered two-dimensional (2D) superstructures of colloidal nanocrystals (NCs) can be tailored by the size, shape, composition, and surface chemistry of the NC building blocks, which can give directionality to the resulting superstructure geometry. The exact formation mechanism of 2D NC superstructures is however not yet fully understood. Here, we show that oleic acid (OA) ligands induce atomic alignment of wurtzite ZnS bifrustum-shaped NCs. We find that in the presence of OA ligands the {002} facets of the ZnS bifrustums preferentially adhere to the liquid-air interface. Furthermore, OA ligands induce inter-NC interactions that also orient the NCs in the plane of the liquid-air interface, resulting in atomically aligned 2D superstructures. We follow the self-assembly process in real-time with in situ grazing incidence small-angle X-ray scattering and find that the NCs form a hexagonal superstructure at early stages after which they come closer over time, resulting in a close-packed NC superstructure. Our results demonstrate the profound influence that surface ligands have on the directionality of 2D NC superstructures and highlight the importance of detailed in situ studies in order to understand the self-assembly of NCs into 2D superstructures.