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Following population growth and rapid urbanization, West African cities have become major sources of anthropogenic pollution. Additionally, Saharan dust has had a significant impact, representing a potentially toxic mix of sources for the population. This study characterizes the atmospheric composition and its sources in two African capitals, Bamako, Mali and Dakar, Senegal. TSP, PM₁₀ and PM_2.5 samples were collected during the dry season in 2009 when pollution levels were high: chemical analysis included organic carbon (OC), elemental carbon (EC), ions, and metals. PM_2.5 and PM₁₀ concentrations were 5–10 times and 3–8 times higher, respectively, than the 2005 WHO 24 h standards. Using PCA and PMF methodologies, five sources were identified in each city. In Bamako, traffic (motor vehicles and resuspended road dust) was the prevailing source of PM_2.5 and PM₁₀, accounting for 47% and 45%, respectively. Crustal dust was the second most important source (24–30%), followed by solid fuel combustion (16–13%) and secondary aerosols (10–16%). In Dakar, the following sources of PM_2.5 and PM₁₀ are identified: traffic (49%), mineral dust (16–25%), sea salts (15–20%) and industries (10–11%). Our study provides crucial information about the historical change in source characteristics in these two African cities, which can help for future mitigation strategies.