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Molecular markers or gene mutations that are associated with resistance have been the recent focus for an attempt to promptly determine the establishment of resistance to known and currently used antimalaria drugs. For control managers, the effective management of malaria would involve strategies of interruption of the malaria transmission and/or improved therapeutic management of malaria. To place molecular markers within the context of control programs requires that one recognises the two data pools necessary for effective evidence-based policy change. These include data on socio-economic determinants on the one hand and biomedical data on the other. The markers for clinical efficacy of drugs have principally been genes either associated with transport or metabolism of the drug. In malaria those that have been the most characterised are the Pfcrt, Pfmdrl for the quinolines and the dhfr and dhps genes for the anti-folates. The PfATPase has been suggested to be involved in the recently developed artermisinine based combination therapies (ACT). To consider changes in drug policy, a control manager needs to address: efficacy, transmissibility, disease dynamics, safety, epidemics, tolerability and compliance. Except for safety and tolerability/compliance, molecular markers do provide useful information. However these markers still have to be validated alongside in vitro studies and in many different ecological settings and shown to be stable over time or associated with changing drug efficacy situations. Besides the evidence provided with these tools, the government will be required to ensure a mass education of the population and care providers, and fight against illicit street vendors. The governments will therefore still wary on the resources necessary to occasion an effective switch in drug policy especially at the district level and in the rural areas where meaningful, cost-effective programs are most needed.