Agriculture is one of the major farming activities, representing 32% of the gross domestic product of Madagascar and 74.3% of the population is involved in this activity. Fruit flies of the Tephritidae family are considered as the most destructive pests for agriculture in the country, nevertheless, few data exist on host plants and distribution of those pests. In the present study, we address those questions by conducting a large survey between November 2016 and July 2018 across the six agroecological regions of Madagascar. Fruit and vegetable were sampled from 198 plant species (wild and cultivated) and represented 37,965 fruits from all regions of Madagascar. The infestation index ranged from 0.06 to 538.46 pupae/kg, the infestation percentage was up to 54.84% in some samples, 63 plant species were considered as host of Tephritidae. Twelve fruit fly species were identified, seven of which were previously described as endemic, five species could be considered as widespread (altitudinal gradients between 1 and 1634 m asl) and major pests in Madagascar: Ceratitis malgassa (23 plant species from 12 families), Neoceratitis cyanescens (16 plant species from one family), Bactrocera dorsalis (18 plant species from 12 families), Dacus demmerezi (ten plant species from one family), Dacus vertebratus (six species from one family). Those results are of importance for implementation of control measures.