The use of insects to identify drugs in a cadaver has often been explored in the field of entomotoxicology. There are accurate methods; however, they require a high cost and are very time-consuming. The objective of this study was to develop two methods based on differential pulse voltammetry (DPV) and fluorescence excitation-emission matrix (EEM) spectroscopy to classify necrophagous larvae (Chrysomya megacephala, C. albiceps, Lucilia sp. and Cochliomyia macellaria) containing flunitrazepam. The voltammograms of larval extract samples were analyzed by principal component analysis (PCA), successive projection algorithm (SPA) and genetic algorithm (GA): linear and quadratic discriminant analysis (LDA and QDA). The EEM fluorescence data from larval extract samples were analyzed by 2D and parallel factor analysis (PARAFAC) with LDA. These results suggest that DPV and EEM combined with chemometrics can be used as tools for the classification of flunitrazepam in fly larvae presenting innovative applications.