Ingested-derived DNA (iDNA) from insects can represent a powerful tool for assessing vertebrate diversity because insects are easy to sample, have a varied diet, and are widely distributed. Despite these advantages, the use of iDNA for mammalian detection is still little explored, especially in the neotropical region. Here we aimed to compare the effectiveness of mosquitoes and flies to detect mammals in a semi-controlled area of a Zoo that houses native and non-native species. We evaluated the number of mammal species detected by the iDNA samplers and verified the distance range of each sampler group for detecting the mammal species. To capture mosquitoes and flies we used CDC (Center for Disease Control) and fish-baited plastic bottle traps, respectively, distributed in eight sampling points during five days. Using two mini-barcodes (12SrRNA and 16SrRNA) and the metabarcoding approach, we identified 45 Operational Taxonomic Units from 10 orders. There was no difference between the number of species recovered per individual insect, although the number of flies captured was higher, resulting in more mammal species recovered by this insect group. Eight species were recorded exclusively by mosquitoes and 20 by flies, suggesting that using both samplers allowed a more comprehensive screening of the biodiversity. The maximum distance recorded was 337 m for flies and 289 m for mosquitoes, but the average range distance did not differ between insect groups. Our essay proved to be quite efficient for the mammal detection, considering the high number of species detected with a reduced sampling effort. Thus, combining iDNA from different samplers and metabarcoding can be a powerful tool for mammal survey and monitoring in the neotropics.