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Biomaterials with outstanding mechanical properties including spider silk, wood, and cartilage, often feature an oriented nanofibrillar structure. The orientation of nanofibrils gives rise to a significant mechanical anisotropy which is extremely challenging to characterize, especially for microscopically small or inhomogeneous samples. Here we report a technique utilizing atomic force microscope indentation at multiple points combined with finite element analysis to sample the mechanical anisotropy of a thin film in a microscopically small area. The system we study is the tape-like silk of the Chilean recluse spider, which entirely consists of strictly oriented nanofibrils giving rise to a large mechanical anisotropy. We present the most detailed directional nanoscale structure–property characterization of spider silk to date, revealing the tensile and transverse elastic moduli as 9 GPa and 1 GPa, respectively, and the binding strength between silk nanofibrils as 159 ± 13 MPa. Furthermore, based on this binding strength, we derive the nanofibrils’ surface energy, as 37 mJ/m2, and conclude that van der Waals forces play a decisive role in inter-fibrillar binding. Due to its versatility, this technique has many potential applications including early diseases diagnostics, as underlying pathological conditions can alter the local mechanical properties of tissues.