To determine differences in the distribution of drug resistance mutations in the Plasmodium falciparum chloroquine resistance transporter (pfcrt) and P. falciparum multi-drug resistance 1 (pfmdr1) genes of P. falciparum isolates in Thailand, a study was conducted using polymerase chain reaction-restriction fragment length polymorphism to detect mutations in P. falciparum isolates obtained from three areas with different levels of in vivo mefloquine (MQ) resistance. All isolates carried mutant allele T76 of the pfcrt gene and wild-type allele D1246 of the pfmdr1 gene except for one isolate, which showed the wild-type K76 allele. This isolate was obtained from Chanthaburi Province, an area with high MQ resistance. Relatively low rates of the mutant alleles D1042 and Y86 of the pfmdr1 gene were found among Thai isolates of P. falciparum. However, a statistically significant difference in the distribution was noted. Most of the mutant isolates were found among isolates from areas with moderate or low MQ resistance. Only one isolate with mixed mutant and wild-type N1042 and D1042 and two mutants of Y86 were found among the isolates from areas with high MQ resistance. The findings provide limited support for the hypothesis that mutant alleles of pfmdr1 may be associated with increased sensitivity to MQ. © 2005 Blackwell Publishing Ltd.