The horticulture industry in Benin is under threat due to fruit fly infestation on important crops such as cucurbits and mango. Given the economic losses due to fruit fly infestations, population dynamics of fruit flies on these crops were monitored over 6 years (2004–2010) using three parapheromones—cuelure, methyl eugenol and terpinyl acetate. A total of 2,714,186 specimens belonging to 14 species in four genera (Bactrocera, Ceratitis, Dacus and Zeugodacus) were collected. Bactrocera dorsalis was the dominant species that accounted for 89%, 89.6% and 77.2% of captures in the Forest Savannah Mosaic (FSM), Southern Guinea Savannah (SGS) and Northern Guinea Savannah (NGS) agro-ecosystems, respectively. Shannon index values of species diversity differed significantly among agro-ecosystems, with highest diversity in FSM followed by SGS and NGS. Temperature, rainfall and relative humidity (RH) positively influenced the abundance of Dacus species and Zeugodacus cucurbitae across the three agro-ecosystems. Monthly mean temperatures were in a range suitable for development and reproduction of fruit flies, although minimum temperatures could be below such range, which may explain the lower abundance of fruit fly populations during this period of the year. The abundance of B. dorsalis was negatively correlated with maximum temperature and positively correlated with RH and rainfall. Ceratitis species assemblages were significantly affected by minimum temperatures, rainfall and agro-ecosystem. Populations of B. dorsalis and Ceratitis cosyra dropped drastically in August, while those of Z. cucurbitae and Dacus punctatifrons increased sharply from August. Results of this study provide a platform for developing a comprehensive and sustainable management strategy for B. dorsalis and other fruit flies in the three agro-ecosystems to protect the horticulture industry in Benin.