The highly sensitive surface enhanced Raman spectroscopy was used to study two of the tumorigenic aurora family kinases, Aurora A and Aurora B in sub- picomole quantities. Significantly, the protein-nanoparticle conjugates were shown to be enzymatically active as demonstrated by kinase assays making it suitable for studies of enzymatic processes. The ability to differentiate between two structurally similar homologous proteins further corroborates the sensitivity of the technique. Based on the available structural information we demonstrate here that SERS could be used for direct and ultra-sensitive detection of autophosphorylation. The overall reduction in SERS intensity and presence of bands at ~ 952 and ~ 1076 cm-1 confirmed the phosphorylated state of Aurora A. Thus, for the first time the detection of autophosphorylation in a full length protein, which is critical to attain its active conformation, is being demonstrated through SERS.