| Summary: | Background: Food contaminated with fungi and their toxins is a problem that threatens many developing countries. Kingdom of Saudi Arabia depends on the exported grain and legume seeds. Materials and methods: The study involved examination of 160 samples of rice and maize seeds collected from different locations in the Kingdom of Saudi Arabia. Heterogeneity in the 18s rRNA gene of toxigenic Alternaria sp. and Fusarium sp. was unraveled. The seeds were disinfected and cultured on Potato Dextrose Agar (PDA), Yeast Extract Sucrose (YES) media and incubated at 25 °C/7 days. The isolated fungi were subjected to 18s rRNA gene sequencing. Five toxins were extracted from maize and rice grains infected with isolated fungi. Results: The isolated fungi were identified based on morphological and spores characters as Fusarium sp. and Alternaria sp. Molecular identification based on18s rDNA barcode' was performed due to its high degree of inter specific variability, conserved primer sites and multi-copy nature in the genome. Fusarium sp. produced the highest detected (2070 μg/kg) fumonisin especially in cereal production season 2011. The collected grain from Dammam recorded the highest percentage (5485.2 g/kg) of toxins. Conclusion: This work highlights that 50% of samples were found contaminated with toxins in various concentrations which impose a threat for public health and necessitate rapid identification methods for toxigenic fungi such as 18s rDNA sequencing. Keywords: Alternaria sp., Fusarium sp., Mycotoxins, PCR, 18s rDNA
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