Information on fruit flies is essential for integrated fruit fly control programs, whilst such information remains very limited in Papua. This study aims to determine the species diversity and abundance of fruit flies in agroecosystems (Yuwanain) and secondary forest ecosystems (Ubiyau) in Arso District, Keerom Regency. Sampling locations were determined using purposive sampling. Fruit fly samples were collected using plastic bottle traps baited with methyl eugenol. Observations were conducted during May and June 2025. Four species of fruit flies were found in Arso District: Bactrocera musae, B. umbrosa, B. fulvicauda, and B. dorsalis complex. All four species were found in the agroecosystem area in Yuwanain, whilst in the secondary forest in Ubiyau, only three species were found: B. musae, B. umbrosa, and B. fulvicauda. All species were pests except B. fulvicauda. The Shannon-Wiener species diversity index values for fruit flies in the agroecosystem (H’ = 0.7) and in the secondary forest (H’ = 0.4) were both categorized as low. The Simpson Dominance Index in Yuwanain was classified as moderate (D = 0.636), whilst in Ubiyau it was categorized as high (D = 0.800). In Yuwanain, B. musae was highly dominant (D = 0.617) with a total individual count of 3,080. The dominance of B. musae in Yuwanain was attributed to the abundance of its primary host plant, banana, in the agroecosystem. The evenness index in Yuwanain village was moderate (E = 0.521), whereas in Ubiyau it was low (E = 0.381), indicating that the distribution of individual numbers for each species was uneven in the Secondary Forest. Fruit fly abundance was higher in the agroecosystem of Yuwanain (3,921 individuals) than in the secondary forest of Ubiyau (2,272 individuals). This difference is likely due to the greater diversity of host plants in the Yuwanain agroecosystem, including banana, papaya, jackfruit, citrus, wax apple, breadfruit, and chili. In contrast, the secondary forest of Ubiyau contains fewer naturally occurring host plants, such as the native Papua banana and breadfruit. It can be concluded that the species composition and abundance of fruit flies at certain habitat types were determined by the diversity and abundance of host plants.