The variation in co-occurrence between pests may influence spatio-temporal persistence strategies of species, with implications for pest management. The co-occurrence of Anastrepha species (Diptera: Tephritidae) in papaya orchards was investigated in areas at different distances from a native forest reserve in Espírito Santo, Brazil, to investigate positive, negative, or random interactions, understood as potential coexistence, interspecific competition, or neutral interactions, respectively. Data were obtained from a papaya-growing area divided into three sub-areas -a buffer zone bordering the forest, neighbourhood 1, and neighbourhood 2 -and the co-occurrence results were compared with the entire area. The buffer zone along the protected native Atlantic Forest (semideciduous seasonal forest vegetation) was created to filter negative environmental impacts. Neighbourhood 1 was closer to the forest than neighbourhood 2. Based on a long-term dataset from 1998 to 2010, co-occurrence of fruit flies was investigated by comparing two periods: from 1998 to 2003, when a special pest management system was implemented, termed the systems approach, and from 2004 to 2010, showing the impact of this system on fruit fly diversity. The strength of interaction between species was also evaluated for significant co-occurrences. The patterns of co-occurrence and interaction of Anastrepha species were influenced by area and time. In all scenarios, only positive and random associations were observed, with Anastrepha fraterculus (Wiedemann) and Anastrepha obliqua (Macquart) showing the most positive associations. Co-occurrence was greater in areas farther from the reserve. However, the strength of the interaction between the areas showed little variation. We concluded that the distance from the reserve and the pest management (systems approach) influenced co-occurrence, as species co-occurred much more frequently when collected far from the native forest. The impact during the period of the systems approach (1998-2003) provided fewer positive associations, but with stronger interactions over time. These results confirm that identifying pest co-occurrence distribution patterns in crops and the respective neighbourhoods can be helpful in improving strategies for pest management associated with a systems approach.