Fruit flies are major economic pests that hinder the increased production and commercialization of fruits and vegetables in Swaziland. However, the diversity and abundance of these nagging pests in the country have not been documented. This underscores the importance of inventorying the fruit fly species in the country as a prelude to formulating a sustainable management strategy of these pests.Asurvey was therefore conducted to detect, collect and identify the various fruit fly species in fruited feral marula and guava using three baits, i.e. vinegar, brewers' waste and commercial fruit fly bait at Ntondozi and Gebeni. Sites were sampled weekly from January to May 2012 when the target plants grew in abundance. Overall, a total of 4168 fruit flies (23 species) were trapped. There were significant differences in the number of flies collected between sites (P = 0.0002). Fewer flies were trapped from Gebeni (1569; 22 species), compared to Ntondozi (2599; 18 species). Ceratitis rosa was the dominant species at both sites and host plants, making up 68.8 % of the overall catch, followed by C. cosyra. Of the dacines, Dacus bivittatus was the dominant species. At Gebeni, there were no significant differences in the number of flies trapped between baits (P=0.1231) while significant differences were observed at Ntondozi (P=0.0009), where the traps with commercial bait had the highest number of fruit flies followed by the brewers' waste and then the vinegar-baited traps. Traps placed on marula trees had a significantly lower number of fruit flies and diversity (1095 fruit flies, 11 species) compared to those placed in guava trees (3073 fruit flies, 22 species) (P=0.000). Host-plant surveys indicated that only C. cosyra emerged from marula fruits while co-occurrence of C. rosa, C. capitata and C. cosyra was observed in guava fruits. The results of this study could formthe basis for the development of a low-cost integrated management package for the suppression of fruit fly populations in Swaziland.