Background. A recovery in chloroquine efficacy following a period of cessation has raised the possibility of its reintroduction for malaria chemotherapy. We investigated the prevalence of the major markers of chloroquine resistance years after the withdrawal of the drug in Nigeria. Materials and Methods. Finger prick blood samples were collected from participants presenting with symptoms of malaria in two selected health centres each representing Lekki and Ijede communities of Lagos, Nigeria. Thick and thin blood smears were prepared for microscopy and dry blood spots made from malaria-positive participants for parasite DNA extraction. The detection of mutations in the Plasmodium falciparum chloroquine resistance transporter (pfcrt) and P. falciparum multidrug resistance (pfmdr1) genes was performed by nested polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP). Results. Of the 1527 blood samples that were confirmed by PCR to be P. falciparum positive, 412 and 344 were typed for the molecular detection of pfcrt and pfmdr1 gene mutations, respectively. The mutant alleles of pfcrt were present among 290 (70%) parasite carriers while the pfmdr1 mutant allele was found in 117 (34%) of the total population. There were higher distributions of the mutant alleles for the two loci in Ijede than in Lekki. The observed frequencies of pfcrt mutant alleles in the two parasite populations were in agreement with the expected frequencies predicted by Hardy-Weinberg. In comparing data with studies conducted between 2000 and 2002 in Ijede, we observed an increase in the prevalence of mutant type pfcrt against a marginal decline in the pfmdr1 mutant type. Conclusion. The high frequencies of pfcrt mutation are suggestive of a persistent drug pressure and continuing inefficacy of chloroquine as an antimalarial drug.