Mutatons on pfmdr1 gene have been implicated in drug resistance to chloroquine and the partner drugs in artemisinin-based combination therapies (ACTs), hence the need to evaluate the impact of ACTs five years after its adoption in Nigeria on pfmdr1 polymorphisms and parasite diversity. Parasite genomic DNA was isolated from children below 5 years in Ibadan in 2010. Nested PCR followed by restriction fragment length polymorphism (RFLP) detected pfmdr1 Y86, F184 and Y1246 mutant alleles were present in 27%, 56% and 48% of the isolates respectively, while nested PCR evaluated polymorphic regions of MSP-1, MSP-2 and GLURP genes and monoclonal infections were observed in 81.6%, 51.6% and 5.6% with multiplicity of infection being 1.8, 2.0 and 2.4 respectively. This study showed a relative decline in the prevalence of Y86, F184 and Y1246 mutant alleles, but no significant change in the parasite population diversity of P.falciparum in children in Ibadan, Nigeria.