For sensitive surface plasmon resonance (SPR) sensing the choice of the metal film and the strategy to bind the receptors to the SPR chip is critical. We have shown recently (Touahir, L.; Niedziolka-Jonsson, J.; Galpin, E.; Boukherroub, R.; Gouget-Laemmel, A. C.; Solomon, I.; Petukhov, M.; Chazalviel, J.-N.; Ozanam, F.; Szunerits, S. Langmuir 2010, 26, 6058) that a 5 nm thick layer of an amorphous silicon-carbon alloy (a-Si1-xCx:H) deposited on a silver-based SPR interface can significantly enhance the sensitivity. In addition, the capping of a surface-plasmon active silver layer with a thin film of hydrogenated amorphous silicon-carbon alloy provides a practical solution for obtaining chemically stable SPR interfaces usable in conditions typical of bioassays with the additional advantage of benefiting from well-controlled processes for a robust covalent immobilization of biological probes to the interface. In this paper we demonstrate that the developed architecture in conjugation with an optimized surface functionalization scheme allows for a highly sensitive analysis of interfacial DNA-DNA binding interactions using surface plasmon-enhanced fluorescence (SPFS) as detection principle. The influence of the density of surface linked DNA probes on the recognition of 50 nM cDNA strands is presented. On an optimized surface (15% of acid-anchoring groups) DNA complementary probes with concentrations of 500 fM could be detected making this approach interesting compared to classical SPR experiments where nanomolar (nM) detection limits are conventionally reached.