Seed-borne fungi are extremely dangerous to agriculture and food safety due to their ability to decrease seed viability, increase food spoilage after harvesting, and release potentially toxic mycotoxins into the food chain which ultimately affect crop productivity and health. Of special concern are Aspergillus species which are very widely distributed and can survive in unfavourable conditions during storage. This study was aimed at isolating, identifying and molecularly characterizing Aspergillus species that were linked to melon (Cucumis melo) seeds that were harvested in the Penjwen area. The fungal isolation was conducted by use of agar plating method on the potato dextrose agar (PDA) and then the initial identification was done by considering the macroscopic and microscopic features. Six different species of Aspergillus were observed A. flavus, A. niger, A. corrugatus, A. fumigatus, A. terreus, and A. tamarii, of which A. flavus was the most common species (30%). Polymerase chain reaction in the form of amplifying internal transcribed spacer (ITS1/ITS4), large subunit ribosomal RNA (LSU) and 2-tubulin (Bt2a/Bt2b) genes was used to perform molecular identification. Agarose gel electrophoresis was able to successfully amplify and confirm the products of the PCR as expected: the products were approximately 650 bp in the case of ITS, 1200 bp in the case of LSU, and 495 bp in the case of 8 -tubulin. The identity of the species was further confirmed by sequencing and phylogenetic analysis which helped to support the evolutionary relations among the isolates. The A. flavus and other Aspergillus species prevalence shows their high adaptability to dry seed conditions and possibilities of producing spoilage-related enzymes and secondary metabolites. The findings demonstrate the significance of the adoption of the best seed handling, storage, and management to reduce fungal contamination and secure a high level of seed quality and food safety.