This paper summarizes the different host plants and fruit flies present in two islands (Grande-Comore and Mohéli) of the Comoros Archipelago. Different exotic and wild fruit plants were sampled. Eighty plant species, potential hosts, belonging to thirty-four families were collected and incubated for the emergence of fruit flies from December 2019 to September 2020. Twenty-five plant hosts from ten families comprising cultivated and wild fruits have been identified. Fruit fly infestation rates per kilogram of fruit (T.Kg-1 ) varied from plant to plant. Exotic fruit plants, which accounted for more than half of infested plants, including Cucumis melo, Cucurbita pepo, Prunus persica, Coffea arabica and Capsicum frutescens had high infestation rates. For wild plants, the highest infestation rates have been observed in some families including Combretaceae, Cucurbitaceae, Solanaceae and Vitaceae. The highest infestation rate per kilogram of fruit was observed in a wild plant: Cyphostemma lageniflorum. Thirteen new host plants infested by Tephritidae are reported and/or listed for the first time in Comoros. In total, eight species of fruit flies identified. However, the species Bactrocera dorsalis Hendel, 1912 (47.5%) and Dacus bivittatus (Bigot, 1858) (37.6%) were the most representative of the Tephritidae that emerged.