Weeds are the major biotic constraint for lowland rice production systems in Togo, particularly in the Savannah region where rice cultivation follows traditional practices with very little mechanization or synthetic pesticide treatment. In order to identify and categorize weed flora of this agricultural system, vegetation surveys were conducted in Northern Togo’s lowlands during the growing seasons of 2012 and 2013. Full floristic surveys were conducted in 33 lowland sites, selected for their accessibility and importance in terms of rice production. A total of 97 weed species from 26 plant families were recorded in 2012 against 103 weed species in 28 families in 2013. The families Poaceae and Cyperaceae were the most represented with 39% and 34% of the total species respectively in 2012 and 2013. Hyptis spigicera Lam. (Lamiaceae), Paspalum scrobiculatum L. (Poaceae), Ludwigia hyssopifolia (G. Don) Excell (Onagraceae) and Rhamphicarpa fistulosa (Hochst.) Benth. (Orobanchaceae) were among the most common species in 2012 and 2013. Species accumulation curves for each season show that more than 75% of total species are recorded after 10 sampled lowland sites. The average species richness in these lowlands is quite similar for the two seasons (22 species in 2013 versus 24 in 2012). Diversity indices of Shannon and Simpson values and the Hill numbers for different lowland sites show that species richness varies among lowland sites and between growing seasons. Finally, we can conclude that the weed flora of Northern Togo rice cultivation lowland areas is very rich and diverse. Our study shows presence of species characteristic of hydromorphic valley bottoms and of rain-fed lowland areas.