The positive selection of a nucleotide substitution in exon 2 of Plasmodium 
falciparum chloroquine resistance transporter (pfcrt) gene (mutation responsible 
for chloroquine resistance) causes a reduction in variation of neutral loci 
close to the gene. This reduction in allelic diversity around flanking regions 
of pfcrt gene was reported in worldwide chloroquine resistant isolates and 
referred as selective sweep. In Plasmodium falciparum isolates of India, the 
selective sweep in flanking loci of pfcrt gene is well established, however, 
high allelic diversity observed in intragenic microsatellites of pfcrt gene 
implied an ongoing genetic recombination. To understand, if molecular evolution 
of chloroquine-resistant P. falciparum isolates in India follow a selective 
sweep model, we analyzed genetic diversity at both seven intragenic and seven 
flanking microsatellites of pfcrt (-24 to +106kb) gene in chloroquine sensitive 
and resistant parasites originating from high and low transmission areas. We 
observed low expected heterozygosity at all loci of resistant pfcrt-haplotypes 
(He=0-0.77) compared to the wild-type (He=0.38-0.96). Resistant SVMNT from high 
transmission areas showed significantly higher mean He (P=0.03, t-test) at both 
intragenic and pfcrt-flanking loci (-24 to +22 kb) in comparison to low 
transmission areas. Our observation of reduction in variation at both intragenic 
and flanking loci of mutant pfcrt gene confirmed the selective sweep model of 
natural selection in chloroquine resistant P. falciparum isolates in India.