Despite progress in the control of malaria, it remains a serious public health problem. Substantial declines in malaria transmission, morbidity and mortality have nonetheless been reported in several countries where new malaria control strategies have been implemented. We conducted this molecular and epidemiological analysis of malaria in the pediatric department of the Chinese-Gabon Friendship Hospital (HCGC) in Franceville in 2010. Franceville is the third largest town in Gabon, and malaria transmission is high year-round. We included 945 children, 756 of them febrile. Malaria was diagnosed based on the detection of P. falciparum in thick blood films, with Lambarene's method. Malaria prevalence among the febrile children included in this study was 17.9% (n=135). The burden of malaria is thus lower than in the past; it is now the second leading cause of pediatric hospital visits, rather than the leading cause as it was in 2004. The children's mean age was 48.5 ± 3.9 months, older than in 2004 (p<0.05). We also analysed the molecular drug resistance marker, Pfmdr1. The prevalence of the wild-type genotype N86 of Pfmdr1 was 47.4% (n=64), higher than in 2004 (p<0.001). The increased prevalence of codon 1246 was not significant. Socio-economic factors and known malaria risk factors were analysed. We found that the use of Insecticide-treated mosquito nets and the provision of information (education or communication) to parents and guardians about malaria were protective factors against the disease. In conclusion, a larger study of the entire region over a longer period is necessary to characterise malaria in Franceville today. Transmission factors must also be studied.