We advocate the use of drosophilid flies as biological models on biological conservation by presenting a case study in the Cerrado at landscape scale. We analyzed the drosophilid assemblage in the Parana Valley, together with a baseline data from Federal District. We found four different drosophilid assemblages structured in both local and regional scales. Our study confirms the importance of the Parana Valley as a diversity center, and the urgency in creating reserves in the region to protect its biological uniqueness. Analyzing drosophilid assemblage composition could help for understanding Cerrado biodiversity by perceiving and focusing it in different scales, and therefore, helping for more accurate and efficient reserve selection, design and placement. Drosophilids can be very useful to study the patterns and processes related to biodiversity and also how human activities affect it, permitting the elaboration of efficient conservation strategies, and improving projections about what might happen in the future.