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Surface plasmon resonance depends on the dielectric medium at the vicinity and makes it a quasi-universal detector. Therefore, and due to the label-free nature, SPR is a widely used sensing tool for real‐time monitoring molecular interactions of various analytes. However, detection of highly diluted analytes and small molecules (< 400 Da) is still challenging. Gold nanohole arrays provide plasmonic hotspots with improved surface sensitivity and 2D carbon nanomaterials enable binding near the surface. Both effects together are promising in the development of SPR sensors for the efficient determination of small molecules. Graphene is known for efficient binding of molecules with delocalized aromatic π-systems. Additionally, the electromagnetic field is locally enhanced and modulated by the interaction of graphene photonics with the plasmonics of metal nanostructures. The advantages of chemical vapor deposition (CVD) graphene over reduced graphene oxide (rGO) is illustrated by a proof of concept study. In comparison to substrates consisting of a continuous film the surface sensitivity is enhanced for a nanohole arrays and further improved for CVD graphene functionalization in contrast to rGO. The feasibility of the sensor was demonstrated for the detection of adenine down to a concentration of 0.9 μM.