Multiplexed detection of biomarkers for cancer and chronic inflammatory diseases is necessary to improve diagnostic sensitivity and specificity. Our prior studies and that of others has used near-infrared fluorescent single-walled carbon nanotubes (SWCNT) as sensor transducers because of their sensitivity to the local environment, photostability, and emission in the tissue-transparent window. That work engineered the SWCNT surface through non-covalent interactions with short ssDNA oligonucleotides containing a functional group to which a biomarker-specific antibody was conjugated. Further, previous work by other groups has demonstrated the ability to obtain single SWCNT chiralities using the aqueous two-phase extraction (ATPE) technique with non-functionalized ssDNA sequences. Here, we have incorporated primary amine-functionalized ssDNA sequences into the ATPE separation technique to obtain individual SWCNT chiralities with functionalized ssDNA. To those primary amine-functionalized ssDNA-SWCNT complexes, we conjugated antibodies against two inflammatory cytokines. We investigated the sensitivity and specificity of these individual SWCNT chirality sensors specific to two biomarkers together in buffer and serum, finding that each chirality responds specifically only to its cognate biomarker and not the other. This is the first demonstration of single-chirality, molecularly-specific multiplexed SWCNT sensors. It forms the basis of ongoing work to obtain additional chiral species with other functional groups, as well as to develop multiplexed cytokine sensors for in vivo diagnostics.