We explored the genetic regulator at the protein level, which responds to aluminum stress in the presence of ectomycorrhizal fungi, Suillus luteus, in the masson pine. Comparison of different treatments, i.e., SL-04 vs CK-04, SL-04 vs SL-0, and SL-0 vs CK-0 resulted in the identification of Al-stress responsive proteins viz. chlorophyll a-b binding protein, laccase, and heat shock protein. Significant gene expression pattern of differentially up-regulated proteins laccase and putative spermidine synthase provide the evidence and explain the role of these proteins in response to Al-stress. Further, based on top differential proteins from each comparison recognized the two common regulators among the differential proteins viz., putative spermidine synthase, Chlorophyll a-b binding protein. This study provides the theoretical basis and understanding of the role of genetic regulators in response to Al stress in masson pine.