Merozoite surface protein 2 (MSP2) is a disordered blood-stage vaccine antigen of the human malaria parasite, Plasmodium falciparum. Antibody recognition of the conserved N-terminal region epitope is limited by transient interactions with the central variable region of MSP2 and structural constrains imposed by membrane binding (1). The conserved C-terminal region of MSP2, with a single disulphide bond, is another focal point for protective immunity. However, similar to the N-terminal region, antibodies against C-terminal epitopes differ in their ability to recognise the native MSP2 on the parasite surface (2). In this work, we explore the molecular mechanisms underlying the marked discrimination of two overlapping epitopes within MSP2207-222 region by the monoclonal antibodies (mAbs) 4D11 and 9H4. The mAb 4D11 is able to bind this region with high affinity irrespective of the presence of the disulphide bond and readily recognise both native and recombinant MSP2 in both immunofluorescence assay (IFA) and surface plasmon resonance (SPR). In contrast, 9H4 requires the disulphide bond for its binding but show affinities 10-fold weaker than 4D11 to recombinant and parasite MSP2 as measured by IFA and SPR. The mechanism of binding of mAbs 4D11 and 9H4 was explored with a panel of synthetic 16-residue peptides mutated at each non-cysteine residue to an alanine. Our data pinpointed residues neighbouring Cys219 and Cys211 essential for 4D11 and 9H4 respectively. Interestingly, mutations able to block 4D11 binding improved the affinity for 9H4 by 1000-fold. Finally, 1H-15N HSQC NMR experiments on mutated peptide epitopes indicate that residues responsible for increased affinity for 9H4 are significantly shifted, suggesting that the small increase in the local flexibility facilitates a tighter binding to the mAb 9H4. Understanding the mechanisms of antibody binding to disordered peptide epitopes from protein such as MSP2 is a major step in the rational structure-based design of better malaria vaccines.