Fungi are the second largest group of eukaryotic organisms, ranging from 1.5 to 5.1 million species. Mycotoxins are chemical rich, stable and tolerate secondary fungal metabolites found in all food processing. Mycotoxin contaminations emerge in the food chain due to infection of agricultural commodities with moulds. Horticultural products are economically and nutritionally important crops that contaminate their products with both toxigenic and pathogenic fungi and produce a variety of mycotoxins. Unfortunately, for taxonomic specialists, identification of closely related species is an overwhelming challenge. Using multilocus sequence analysis (MLSA), molecular identification, genome sequences and genetic variability among fungal complex creates molecular markers that solve taxonomic difficulties. In addition to food, molecular detection of mycotoxins may serve as good alternatives to conventional methods that target their biosynthetic pathway for spotting horticultural products to ensure food protraction and food security. Frequently polluted contaminants are aflatoxins (AFs), ochratoxins (OTs), patulin (PAT), citrinin (CIT), zearalenone (ZEA), fumonisisns (FUM) and trichothecenes (TRI). Because of the high public concern about chemicals/metabolites from microbes in food today, end-product consumers have to beware of their adverse effects. However, nutritional formulations for children and infants based on fruits and vegetables demonstrate the vital impact on their physiology. In fact, these horticultural products are highly contaminated with complex obscure toxins. Mycotoxin detection is another significant problem in the food industry, including fruit export and import. Nanobiotechnology has recently been developed for a wide range of applications in the diagnosis, detection and management of pathogens in agriculture. Furthermore, magnetite nanoparticles for the detection of mycotoxins are more advantageous for nanosensors. Using aptamers (Apt), the novel fast, responsive and field-deployable rapid point-of-care diagnostics precisely recognizes and binds its targets via novel nanobiotechnological approaches.