© 2017 Taylor & Francis. Mycoplasma pneumoniae is a human respiratory tract pathogen causing chronic bronchitis and atypical or “walking” pneumonia. The major surface protein P1 must form complexes with proteins P30 and P40/P90 to function in receptor binding and gliding motility, and variability in P1 and P40/P90 distinguishes the two major M. pneumoniae genotypes. Strains belonging to each genotype can be differentiated with high sensitivity and specificity by utilizing surface-enhanced Raman spectroscopy on silver nanorod arrays. Here, we used the variable selection method of variable importance in projection (VIP) to identify Raman bands important in M. pneumoniae strain classification. Furthermore, VIP analysis of mutants lacking P40/P90, or P1 and P40/P90, correlated certain Raman bands important in distinguishing genotypes, with specific mycoplasma surface protein composition and presentation. Variable selection, and its correlation with specific mycoplasma surface components, is an important next step in developing this platform for M. pneumoniae detection and genotyping.