The malaria parasite Plasmodium falciparum utilizes host glycosaminoglycans (GAGs) as receptors for erythrocyte invasion and intravascular sequestration. Heparin and heparan sulfate (HS) are GAGs which can block erythrocyte invasion of the P. falciparm merozoite, albeit the molecular mechanisms remain poorly understood. Characterization of these heparin-binding merozoite proteins and key ligands in the host–parasite interplay will lead to a better understanding of the mechanism of erythrocyte invasion by malaria parasites. Here, schizont-derived proteins that bind heparin were enriched by affinity chromatography, and 6062 peptides from 811 P. falciaprum-derived proteins were identified by two-dimensional liquid chromatography–mass spectrometry (LC/LC–MS/MS). The proteins were categorized into 14 functional groups ranging from pathogenesis, protein catabolic process to signal transduction. Proteins with predominant peptide counts were found to mainly originate from the rhoptry organelle of merozoites and the parasitized erythrocyte membrane. The profile of the heparin/HS-binding proteome of P. falciparum suggests they have important functions in the biology of the parasite.