The emergence and spread of drug-resistant parasites are major problems that prevent the control of malaria. Parasite resistance to most anti-malarial drugs, such as chloroquine, sulphadoxine-pyrimethamine, quinine, and mefloquine, has increased globally, rendering these drugs useless in most malaria-endemic areas (Wongsrichanalai et al. 2002). The World Health Organization currently recommends artemisinin-based combination therapy (ACT) as the first-line treatment for malaria; however, a decline in the effectiveness of ACT was recently reported in the border region between Thailand and Cambodia, indicating the emergence of an artemisinin-resistant parasite (Dondorp et al. 2009; World Health Organization 2010). If such drug-resistant parasites become widely distributed, global malaria control efforts will be significantly hampered. The identification of genes responsible for drug resistance is crucial for combating drug-resistant parasites because the mutations found in these genes are useful molecular markers for the surveillance of the emergence and spread of drug-resistant parasites. In the past, the identification of resistance genes was carried out by restriction fragment length polymorphism (RFLP) analysis of the progeny generated by genetic crosses between drug-resistant and drug-sensitive parasites using primates and mosquitoes. The chloroquine-resistance gene (pfcrt, MAL7P1.27) of Plasmodium falciparum was identified by this approach and facilitated the elucidation of the mechanisms of chloroquine resistance and the global surveillance of this resistant parasite (Wellems et al. 1991; Su et al. 1997; Djimde et al. 2001a,b). However, because this approach requires a large amount of time and effort, resistance genes for other anti-malarial drugs, such as mefloquine and quinine, have not yet been identified. Moreover, unknown resistance genes are thought to be present even in the chloroquine-resistant parasite (Valderramos et al. 2010). Now, whole-genome sequencing and microarray technologies are used for the identification of single nucleotide polymorphisms (SNPs) involved in the drug resistance of parasites (Hunt et al. 2010; Rottmann et al. 2011). However, it may be difficult to identify the drug-resistance genes from field-isolated parasites using these two technologies because these parasites have more than 10,000 SNPs (Dharia et al. 2010). Therefore, a more effective method for the identification of drug-resistance genes in parasites is required. The artificial chromosome—which consists of three essential elements, the centromere, the telomere, and the replication origin—is an attractive genetic tool for molecular biology–based studies in eukaryotes. The first eukaryotic artificial chromosome was developed in the budding yeast Saccharomyces cerevisiae and is known as the yeast artificial chromosome (YAC) (Murray and Szostak 1983). The YAC can be stably maintained throughout mitosis and meiosis and has been widely used for cloning large DNA fragments. The development of artificial chromosomes in other eukaryotes, including humans, has been attempted by combining these three essential elements but has not yet been successful. Human artificial chromosomes are integrated at the centromere or the telomere of the original chromosome during cell division and are therefore not episomally maintained (Ikeno et al. 1998). In a previous study, we made a Plasmodium artificial chromosome (PAC) from the small centromere (1189 bp) and the short telomeric fragment ( 99.9% efficiency during multiple rounds of cell divisions. After cell division, it is stably maintained as a single copy without integration throughout the parasite life cycle. Notably, the transfection efficiency of the PAC is significantly higher than that of a normal plasmid. These unique features of the PAC overcome the current technical limitations of parasite genetic modification technology and could be applied in various parasite research fields. In the present study, we demonstrate that the PAC can be utilized for the identification of drug-resistance genes from parasites. Finally, we discuss the advantages of the method for identifying drug-resistance genes.