Drug resistance against P. falciparum has been recognized as the crucial obstacle to curbing mortality and morbidity from malaria. We therefore determined the baseline distribution of pfcrt and pfmdr1 genes associated with resistance to chloroquine and pfdhfr gene associated with resistance to pyrimethamine in P. falciparum isolates collected from two geographically distinct areas of Nigeria. We use RT-PCR assays and sequencing to determine the prevalence of these mutations. The combined prevalence of pfcrt T76 mutation in the two sites was 92.3% with 86% from Osogbo compared to 93% from Lafia. Sequencing analysis of the (Pfcrt) K76T haplotype (amino acids 72-76) revealed CVIET as the only resistance haplotype present in the two areas. The frequency of pfmdr1 polymorphisms was higher in Lafia (39%) compared to that in Osogbo (35%) and the combined prevalence from the two sites was 45.5%. The prevalence of the pfdhfr triple mutant alleles was high in both locations. The Osogbo vs Lafia prevalence for pfdhfr mutations was 84% vs 91%, 88% vs 87% and 96% vs 96% for I51, R59 and N108, respectively. None of the samples from the two locations had the T108 mutation. The combined prevalence of pfcrt and pfmdr1 in Osogbo and Lafia was 44.2% with a risk ratio of 0.4164 while the combined prevalence of pfcrt, pfmdr1 and pfdhfr was 40.4% with a risk ratio of 1.081. These results strongly suggest the widespread distribution of CQ and pyrimethamine resistance without any marked distinction between the two locations.