The sequestration of Plasmodium falciparum in the placenta contributes to multiple placental malaria pathologies. VAR2CSA, a member of P. falciparum erythrocyte membrane protein 1 family of variant proteins, mediates the sequestration via the binding of parasite‐infected red blood cells to chondroitin 4‐sulfate in the placenta. This selective binding makes VAR2CSA a specific target for developing placental malaria treatment strategies. VAR2CSA contains ~310‐kDa C4S‐binding ectodomain, which thought to consist of an N‐terminal segment (NTS), six canonical Duffy‐binding‐like domains (DBL1‐DBL6), and interdomain (ID1 and ID2) segments. The ectodomain contains 116 cysteine residues. Up to eight intradomain disulfide bonds may be observed in canonical DBL domains; however, not all cysteine residues in a DBL domain conform to this pattern and additional ones are located outside the DBL domains. Recent cryo‐electron microscopy reconstructions revealed the functional core structure containing a third interdomain component (ID3) and substantiated the carbohydrate‐binding channel identified earlier. However, up to 46 % of the core, including the paths of ID1, regions of ID2 remain untraced in these structures. Here, by chemical cross‐linking/mass spectrometry of VAR2CSA, we identify additional interdomain interactions in the unmodeled regions of VAR2CSA. Disulfide bond mapping identifies roles for non‐canonical disulfide bonds and reveals previously un‐modelled interdomain disulfide bonds that link ID2 to DBL4ε. In addition, we resolve a disagreement in the interpretation of ID3 by unambiguously identifying the cysteine residues involved in the disulfide bond between DBL4ε and ID3.