Objective To analyze the polymorphism of histidine rich protein 2(HRP II)gene in Plasmodium falciparum (Pfhrp2)from falciparum malaria patients in Yunnan Province,so as to lay the foundation for studying the defection of antigen genes of Plasmodium. Methods The filter paper blood samples and related information of falciparum malaria cases reported were obtained in Yunnan Province from August 2012 to September 2015. Under the guidance of the specific primers,the exon2 regions in Pfhrp2 gene in P. falciparum from DNA samples were amplified by PCR,and the PCR products were sequenced. The sequences of exon2 region in Pfhrp2 gene were blasted by comparing with the reference sequences AY816237,AY816240,and AY816301. Next,the polymorphism of the sequence in exon2 region of Pfhrp2 gene was analyzed by MEGA 5.04 software. The conserved sites and genetic distances between sequences were calculated by using the software as well,and the clustering tree was drawn according to the genetic distances between the amino acid sequences. Results A total of 218 bloods samples from the falciparum malaria cases in 15 prefectures of Yunnan Province were collected,and the sources of infection included Yun?nan,Africa and Myanmar. The PCR results showed that the exon2 regions in Pfhrp2 genes of 155 samples were positive by am?plification and their products were sequenced successfully. The sequence analysis showed that the length range of the amino acid residues of exon2 region in Pfhrp2 gene was from 115 aa to 298 aa,the average length was 239.7 aa. There was no statistically significance among the means of the amino acid residues of the isolates from Africa( 239.9 aa),Myanmar(239.5 aa)and Yun?nan(241.6 aa)(F=0.025,P>0.05). All the 155 amino acid sequences ended with type 12 repeat,98.1%(152/155)of them started with type 1 repeat and 1.9%(3/155)of them started with type 2. Type 2 presented most frequently repeat in all the se?quences and the average repeat times were 12.9. The homologous locus of the DNA sequences in exon2 regions of the 155 Pfhrp2 genes was 894 bp,among which the conservative sites accounted for 20.6%(186/894),and the variable sites for 78.2%(699/894). The genetic distances between the sequences of Africa isolates ranged from 0 to 0.741,and those of the Myanmar and Yun?nan isolates were 0-0.948 and 0-0.750,respectively. The cluster analysis showed that all the 155 sequences clustered into 3 cat?egories on genetic distances between amino acid sequences according to the size of the amino acid sequence length. At the same level,the sequences had approximate lengths and amino acid repeat types. Conclusion The sequence of exon2 region in Pfhrp2 gene of P. falciparum from falciparum malaria cases in Yunnan Province is highly polymorphic,the P. falciparum iso?lates are clustered mainly according to the size of the amino acid sequence of exon2 region in Pfhrp2 gene.