To develop a method for comparing the haplotypes of pfcrt polymorphism of Hainan Province with those from other areas of the world.Nested PCR was used to amplify the polymorphic region including codon 72 to 76 and 97 of pfcrt gene. The PCR products were digested by ApoI restriction endonuclease to determine the allelic types. According to the allelic types, 6 products from each of mutant type and wild type were sequenced to analyze the haplotypes of pfcrt polymorphism.Bands in size of 195 bp appeared in all 19 samples. After ApoI digestion, 11 samples contained one ApoI site when codon 76 of the pfcrt gene codes for lysine (K76), which were visualized by the presence of 98 bp and 97 bp restriction fragments. The DNA sequencing revealed that 6 samples of chloroquine resistant P. falciparum carried pfcrt alleles encoding an amino acid haplotype of CVIET (residues 72-76), and the haplotype of CVMNK was found in other 6 samples with wild type pfcrt gene.Haplotypes of pfcrt polymorphism from Hainan were the same as those from southeast Asia and Africa.