The knob-associated histidine-rich protein (KAHRP) is an exported parasite protein and the major component of infected erythrocytes by Plasmodium falciparum. P. falciparum histidine-rich protein-1 (PfHRP-1) is docked by KAHRP, which this interaction plays a significant role in cytoadherence of the malaria protozoan to erythrocytes and pathogenicity. The most polymorphic region of the PfHRP-1 is the C-terminal of decapeptide repeat domain (region III). The main objective of this study was to explore the genetic diversity at the region III of KAHRP in P. falciparum isolates from Burundi. In the present study, the nested PCR was performed for the amplification of the coding gene (kahrp gene) for region III in 35 P. falciparum isolates from Burundi. The nested PCR products of seven randomly selected isolates were purified and then sequenced. As the result, three allelic forms (340 bp, 370 bp, and 400 bp) were seen at the C-terminal domain of kahrp gene. The existence of multiple alleles of the kahrp gene revealed the presence of different P. falciparum strains in Burundi. It is suggested that the results could be useful in designing and the improvement of targeted therapy agents for falciparum malaria.