Background: In Mozambique, mango (Mangifera indica L.) is the fruit species with highest production after banana, largely by small scale farmers (FAOSTAT 2015). The occurrence of fruit flies including Bactrocera dorsalis (Hendel) and Ceratitis cosyra (Walker) is the most important factor hampering the production of the crop (Ekesi et al. 2009; Cugala 2011). Several studies were conducted in west and east Africa to assess the seasonal fluctuation of the population of the two species indicating that the relative abundance of those flies varies throughout the year. Methods: Fruit flies were monitored over two consecutive mango seasons from September 2014 to August 2016 on 10 hectares of commercial mango orchard in Vandúzi district, Mozambique. Trapping activities were conducted using food attractant (Torula yeast) with Chempac Bucket traps. Climatic and host data were collected at the orchard (temperature, mango phenology) and at a meteorological station (rainfall) located 10 km away over the entire trapping period. Results: Fruit fly populations were present in the orchard over the entire trapping period (B. dorsalis); or absent at some periods during vegetative stages of the mango host (C. cosyra). The population of both species varied between the two seasons, but in general B. dorsalis (FTD = 2.85) was more abundant than C. cosyra (FTD = 0.68). Positive relationships were observed between the population of B. dorsalis with minimum temperature and host phenology, and negative relation with maximum temperature, average temperature and rainfall. Significant relationships were only observed with minimum temperature, average temperature and mango phenology. For C. cosyra, positive relationships were observed with the minimum temperature, maximum temperature and phenology of mango; and negative relationships with the average temperature and rainfall. Minimum temperature was the only factor with significant relationship. Conclusion: The population of B. dorsalis and C. cosyra fluctuated throughout the year and B. dorsalis were more abundant than C. cosyra with some periods of exclusive presence. This fluctuation were related to biotic and abiotic factors.