Every year, about 1 million people worldwide die from malaria, while 300-400 million become infected. The groups suffering most are young children and pregnant women. Malaria''s economic impact is huge, reducing economic growth rate by an estimated 1.3% per year in most endemic areas.In the absence of an effective vaccine, access to safe and effective treatment still remains the mainstay in the control of the disease. However, the efficacy of this control strategy is hampered by the emergence and spread of drug resistant malaria which may lead to excess of mortality. In the present study, we investigated the dynamics of malaria parasite resistance molecular markers in two areas of different transmission intensity with two different drug pressures. The data showed that Antimalarial drug resistance can develop very fast even under very low drug pressure and that the molecular markers could be used as an early warning tool to assess the spread of antimalarial resistance. Thus, careful baseline evaluation of the molecular resistance background could help when drug policy has to be changed.