Knowledge of the diversity of fruit flies is essential for understanding aspects of their community ecology. However, the effectiveness of sampling methods in representing species diversity and relationships with hosts in a diverse environment has not been adequately assessed. This study aimed to determine the optimum method to represent the diversity of fruit flies and assess their relationships with host fruits. Species of Anastrepha sampled with both traps and fruits in the same area were comprehensively analyzed. Data were analyzed by Hill's numbers (species diversity in both sampling methods), heat map graph (interaction of species with methods), and rank clocks (population fluctuations of the most abundant species). We also measured the interaction strength of the species. Our results showed that estimated parameters of species diversity in an area may differ when sampled with traps or fruits. However, the most abundant species appeared to interact similarly in both methods. Fruits of members of the families Myrtaceae and Anacardiaceae contributed highly to the presence of Anastrepha. The optimum strategy to represent Anastrepha diversity in an area is the combined use of both sampling methods.