The aim of this study was to describe the malaria morbidity and the frequencies of molecular markers of resistance to chloroquine and sulfadoxine-pyrimethamine in pregnant women at delivery in Mali. Two hundred pregnant women have been included at the delivery clinic in Fana. The age group of 14-19 years was predominant. Fifty two per cent (52.3%: 104/200) were malaria slides positive in their peripheral blood and 15% (30/200) of the women carried parasite in their placenta. The prevalence rate of anemia was 44.5% (89/200). PCR technique was successfully performed on 16 paired samples. The frequency of the Pfcrt K76T mutants in Plasmodium falciparum infections in peripheral blood was 68.8% (11/16) and 100% (16/16) in the placenta (p = 0.004). The frequency in peripheral blood of the DHFR N51I mutation was 12.5% (2/16) and 18.8% (3/16) in the placenta (p=0.12). The frequencies of the DHPS A437G mutants were similar in both sites 25% (4/16). No DHPS K540E and DHFR 164L mutations were found in the Fana pregnancy women samples.