The aim of the present work is to evidence the role of the linked phospholipids of natural rubber (NR) in the rubber-carbon nanotube (CNT) interactions in rubber composites. Three rubbers namely NR, deproteinized NR (DPNR) and a synthetic rubber isoprene (IR) were used as matrix for CNTs. The selective wetting of CNTs in miscible NR/IR and DPNR/IR blends was investigated by means of the modified wetting concept based on Fourier transformed infrared (FTIR) analysis of the rubber-filler gel of blends. It revealed that the surface of CNTs is entirely wetted by NR or DPNR molecules, respectively, but not by IR. This result emphasizes that proteins do not influence the affinity between NR and CNTs, while the linked phospholipids interact with CNT surface through cation-π linkage. This linkage acts as anchor point supporting NR molecules to wet CNT surface effectively. The modified wetting concept can be used for characterization of selective wetting of different fillers in blends consisting of miscible rubber components.