A better understanding of malaria transmission dynamics is an essential element in the development of any targeted vector control strategy. The objective of this study was to better understand malaria transmission dynamics along the Niger River in Sudan savanna zone of Mali. Trough cross-sectional surveys, Anopheline larvae were collected by WHO standard dipping technique, and vector adults by Human Landing and pyrethrum spray catches methods. The vector population was composed of An. gambiae s.l. (> 99%) and An. funestus (< 1%). An. gambiae s.l. was composed of 96% and 98% of An. gambiae s.s. respectively in Kéniéroba and Fourda. An. gambiae s.s. was in majority composed of its molecular form M in both locations. The density of An. gambiae s.l was higher in the dry season in the immediate vicinity of the river (fishing hamlet Fourda) compared to farther inland Kéniéroba. The average infection rate of An. gambiae s.l. was 3.63% and 4.06% in Kéniéroba and Fourda respectively. The average entomological inoculation rate (EIR) during the study period was almost similar in Kéniéroba (0.70 infective bites/person/month) and Fourda (0.69 infective bites/person/month). The means EIRs over each of the rainy season 2006 and 2007 were always higher than the one of the dry season 2007 in both localities, with much smaller amplitude in Fourda than in Kéniéroba. However, the level of the transmission was 2.31 (0.37/0.16) times higher in Fourda than in Kéniéroba during the dry season.We conclude that in Sudan savanna zone of Mali, malaria transmission along the river is continuous throughout the year, but it is more intense in the immediate vicinity of the river during the dry season than during the rainy season in opposition to more distant localities to the river and vector control should not be focused only on the rainy in such setting.