Filamentous fungi (ff) are a diverse group of unique eukaryotic organisms currently accepted to belong to the Eumycota kingdom. They are ubiquitous in nature with an extraordinary ability to decompose plant wastes while also causing much spoilage of food commodities. Information about each ff, namely, morphological and molecular descriptions, including modern spectral data-MALDI-TOF MS, physiological and biochemical features, ecological roles, and societal risks or benefits is the key element in fungal identification. In order to attain a rapid ff identification in food the genomic and proteomic approaches are currently used. The present paper focus on the main contribution of MALDI-TOF MS to identification spoilage ff in food.