Over the past 10 years, the Mekong Delta region in Vietnam has experienced fast socio-economic development with subsequent changes in malaria vectors ecology. We conducted a 2-year prospective community-based study in a coastal rural area in the southern Mekong Delta to re-assess the malaria epidemiological situation and the dynamics of transmission. The incidence rate of clinical malaria, established on 558 individuals followed for 23 months by active case detection and biannual cross-sectional surveys, was 2.6/100 person-years. Over the 2-year study period, the parasite rate and malaria seroprevalence (Plasmodium falciparum and P. vivax) decreased significantly from 2.4% to almost 0%. Passive case detection (PCD) of clinical cases and serological follow-up of newborns carried out in a larger population confirmed the low and decreasing trend of malaria transmission. The majority of fever cases were seen in the private sector and most were unnecessarily treated with antimalarials. Training and involvement of the private sector in detection of malaria cases would greatly improve the quality of health care and health information system.