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Simple Summary: Tropical rainforest can provide various ecological services to adjacent agricultural environments, including maintaining and amplifying the numbers of beneficial insects. However, forest fragmentation and the selective cutting of indigenous trees used by native species of fruit flies and their parasitoids, degrades the potential of forests to provide ecological services to agriculture. Over a two–year period, we surveyed natural areas of the Mayan rainforest in Quintana Roo, Mexico. We found 11 species of native fruit flies belonging to the genus Anastrepha associated with 25 species of fruits belonging to ten plant families. We report the first records of 10 host plant species of the genus Anastrepha. We also report a new undescribed species of Anastrepha. The interaction between fruit flies and their parasitoids with host plants depends on fruit availability, which is crucial for the survival of each of these species. Our findings indicate that the areas of the Mayan rainforest surveyed represent a highly important reservoir for the diversity of native parasitoids spatially and temporally that are practically absent in fruits of cultivated plants. Conserving the landscape of the Mayan rainforest is important not only for species conservation, but also for the maintenance of fruit fly host plants of biological control agents in orchard agroecosystems in southeastern Mexico. Over a two–year period, we surveyed natural areas of the Mayan rainforest in Quintana Roo, Mexico. We found 11 species of Anastrepha Schiner (Diptera: Tephritidae) infesting 25 species of fruits belonging to ten plant families. We report the first records of 10 host plant species of the genus Anastrepha, which include the first report of a plant family (Putranjivaceae) serving as host of Anastrepha fraterculus (Wiedemann) infesting Drypetes lateriflora (Sw.) Krug and Urb. (Putranjivaceae). Pouteria reticulata (Engl.) Eyma (Sapotaceae) was found, for the first time, to be infested by Anastrepha serpentina (Wiedemann) and by a new undescribed species of Anastrepha. We also report Casimiroa microcarpa Lundell (Rutaceae) as a possible ancestral host for the Mexican fruit fly, Anastrepha ludens (Loew), in Central America. The family Sapotaceae was the best-represented host group with three fruit fly species recovered: A. serpentina, an economically-important species, found in eight host plants, and A. hamata and A. sp. (new species). We recorded six species of koinobiont parasitoids: Doryctobracon areolatus Szepligeti, Utetes (Bracanastrepha) anastrephae Viereck, Opius hirtus Fisher, and Doryctobracon zeteki Musebeck, (all Braconidae), and Aganaspis pelleranoi (Brethés) and Odontosema anastrephae Borgmeier, (both Figitidae). All these parasitoid species represent at least a new report for their host plants. Of the whole parasitoid community, D. areolatus was the most important parasitoid species with 52.7% of presence in 12 host plant species, parasitizing six fruit fly species. The interaction between fruit flies and their parasitoids with host plants depends on fruit availability, which is crucial for the survival of each of these species. Conserving the landscape of the Mayan rainforest is important not only for species conservation, but also for the maintenance of fruit fly host plants in orchard agroecosystems in southeastern Mexico. [ABSTRACT FROM AUTHOR]