Parasite drug resistance remains a great hindrance to effective control of malaria. Despite the widespread resistance, Sulphadoxine-Pyrimethamine (SP) is still used as one of the Artemisin-based combination therapies (ACTs). SP resistancehas been associated with mutations in the dihydrofolate reductase (DHFR) gene of Plasmodium falciparum. We hypothesized that other factors may contribute to the prevalence of DHFR resistant genotypes in areas of limited use of SP in Ibadan,south-west NIGERIA. Blood samples were collected from 100 children presenting with microscopically confirmed P. falciparum. Parasite DNA extracted from dried blood spots by Chelex method was analysed with a primary Polymerase Chain Reaction(PCR) and nested PCR for specific DHFR codons; 108, 51 and 59. Overall, 83% had resistant DHFR 108 genotypes. Mutations in the Ile51 and Arg59 were present in 69% and 76% respectively. The proportion of Ser108 increased significantly with age while the proportion of resistant genotypes Asn108 reduced with age. The prevalence of DHFR alleles differed between genders. Among the females, the prevalence of the Ser108a nd Cys59 increased with age while the prevalence of the Asn108 and mixed infections Ser108/Asn108 decreased with age. There was an increased risk of the Asn108 resistant genotypes being present in the females in a 2: 1 ratio [OR=2.3, 95% CI=1.2-4.5] when compared to the males [OR = 1.0, 95% CI= 0.8-2.1]. This study shows that other factors in addition to drug selection, specifically age and sex, may determine the distribution of DHFR resistant genotypes in areas of limited SP usage.