Ten Tephritid species of economic importance occur in the Comoros Union, including Bactrocera dorsalis (Hendel) that was first recorded in 2005. Comoros Union is composed of three volcanic islands (Grande Comore, Moheli and Anjouan) each with different topography and strong differences in climatic factors within and between islands. Up to now, little was known about the influence of these factors on fruit fly species composition, distribution and interactions on the archipelago. The main objectives of this study were to characterize the population dynamics of fruit flies in relation to seasonality and host fruit availability and the effect of temperature and rainfall on the distribution of fruit fly species. Field was carried in 11 sites across the three islands within an altitudinal range of 55 to 855 meters above sea level for 2 years. Four different lures were used throughout the survey and fruit phenology was recorded weekly. The invasive species B. dorsalis was recorded as the most dominant species followed by Ceratitis capitata accounting for …% and …%, respectively. The population density of the different species was higher during the hot and rainy season than during the cold and dry season. Higher densities of B. dorsalis were observed on Grande Comore Island compared to Moheli and Anjouan where the invasion is probably more recent. The abundance of B. dorsalis was significantly higher in guava and mango compared to the other host species. Bactrocera dorsalis was found to prefer hot and humid areas, while C. capitata preferred dry areas of medium altitude, suggesting niche climatic partitioning between the two species.