Ten economically important species belonging to the Tephritidae have been recorded in Union of the Comoros (an island nation off the coast of East Africa). Little is known about the distribution of these species and how they are affected by climatic factors in the Comoros archipelago. The main objectives of this study were to characterize: (i) the population dynamics of tephritid fruit flies in relation to season and host fruit availability and (ii) the geographic distribution of tephritids in relation to temperature and rainfall. The study was conducted during 2 years at 11 sites on three islands (Grande Comore, Anjouan, and Mohéli) in the archipelago. The site elevations ranged from 55 to 885 m a.s.l. At each site, flies were collected weekly in eight traps (four different lures, each replicated twice). Fruit phenology was also recorded weekly. The dominant tephritid species detected was the invasive Bactrocera dorsalis Hendel followed by Ceratitis capitata Wiedemann. Tephritid species were generally more abundant during the hot and rainy seasons than during the cold and dry seasons. Bactrocera dorsalis numbers were higher on Grande Comore than on the two other islands. On Anjouan and Mohéli, B. dorsalis numbers were very low in 2014 but sharply increased in 2015, suggesting a recent invasion of these islands. Abundances were significantly related to the fruiting of mango, strawberry guava, and guava for B. dorsalis and to the fruiting of mango, guava, and mandarin for C. capitata. Bactrocera dorsalis was more abundant in hot and humid low-altitude areas, while C. capitata was more abundant in dry medium-altitude areas, suggesting the occurrence of climatic niche partitioning between the two species.