Early virus identification is a key component of both patient treatment and epidemiological monitoring. In the case of influenza A virus infections, where the detection of subtypes associated with bird flu in humans could lead to a pandemic, rapid subtype-level identification is important. Surface-enhanced Raman spectroscopy coupled with machine learning can be used to rapidly detect and identify viruses in a label-free manner. As there is a range of available excitation wavelengths for performing Raman spectroscopy, we must choose the best one to permit discrimination between highly similar subtypes of a virus. We show that the spectra produced by influenza A subtypes H1N1 and H3N2 exhibit a higher degree of dissimilarity when using 785 nm excitation wavelength in comparison with 532 nm excitation wavelength. Furthermore, the cross-validated area under the curve (AUC) for identification was higher for the 785 nm excitation, reaching 0.95 as compared to 0.86 for 532 nm. Ultimately, this study suggests that exciting with a 785 nm wavelength is better able to differentiate two closely related influenza viruses and likely can extend to other closely related pathogens.