Plasmodium falciparum chimeric protein 2 (PfCP-2), fused by erythrocytic stage antigens, AMA-1(III) and MSP1-19, is a potential vaccine candidate against malaria. However, the two-band pattern of this protein product in SDS-PAGE has some negative influence for the application of it for clinical tests. N-terminal sequence analysis of the product showed that the doublet had different N-terminus, with 9 amino acid deletion in the band with low molecular weight. Therefore, the gene was modified to generate a new construct, named PfCP-2.9, which was lack of these 9 residues at its N-terminus. Expression of PfCP-2.9 produced only one band. Moreover, the new construct was as same as the original product in the level of expression, conformation dependence on the disulfide bond, immunogenicity and inhibitory effect on the parasite growth in vitro.