The Sudano-Sahelian zone of Cameroon is characterized by a hot tropical climate and poor sanitation, favorable to the proliferation of synanthropic flies and endemicity of diarrheal diseases. Through their activities, proliferating flies can increase the transmission of diarrheal diseases in the region. This study aimed to determine the factors that influence the variation in the diversity and dynamics of synanthropic flies to contribute to the control of diarrheal diseases. Monthly capture of synanthropic flies was carried out at 63 stratified randomly selected sites over nine months, covering both rainy and dry seasons. Three baits of 40 g each were used to attract the flies. All flies attracted to each bait were captured using a trap after 5 min of exposure and identified using the usual identification keys. Data on altitude, rainfall, temperature, humidity and wind speed of each catching site were collected for their potential impact on fly activity. Fifteen synanthropic fly species were identified in this study. These insects were more abundant in July and August in endemic cholera areas, and areas with high human density. They were less abundant in January and February in low-human density and agricultural areas. The diversity of these insects was heterogeneous and sparsely distributed (Shannon diversity index H'=1.57, and Equitability of Pielou index J = 0.63). Simpson’s dominance diversity index was D = 0.57, indicating that Musca domestica was the most abundant species. Human density and the rainfall were the major factors influencing the structure of synanthropic fly communities in the study site.