Agricultural products may be contaminated by mycotoxin-producing pathogenic fungi while on the field or during harvesting and storage. A field survey was conducted in order to isolate and identify the mycotoxin-producing fungal strains in melon seeds collected from major markets in eight States in Nigeria. Samples per site were pooled, processed and screened for the presence of mycotoxin-producing fungi by culture technique and Internal transcribed spacer sequencing (ITS).  Mycotoxin production was determined using thin-layer chromatography (TLC) with a scanning densitometer.  Eighteen producing fungi species:  Macrophomina phaseolina, Aspergillus foetidus, Aspergillus flavipes, Rhizopus oryzae, Aspergillus flavus, Aspergillus niger, Penicillium aurantiocandidum, Aspergillus awamori, Neurospora crassa, Aspergillus fischeri, Aspergillus flavus, Aspergillus tamarii, Aspergillus oryzae, Lichtheimia hyalospora, Aspergillus terreus, Rhizopus oryzae, Aspergillus welwitschiae, Aspergillus corrugatus were identified. These sequences with accession numbers between MN423295-MN423331 have been deposited at the National Center for Biotechnology Information (NCBI) database. The genera Macrophomina and were the most dominant.  Some of the identified fungi are noted for the production of mycotoxins and mycotoxins exert toxic effects on animals and humans. The fungi associated to melon seeds diseases were identified and can be taken as targets in the varietal improvement of melon seeds for resistance to fungal diseases in Nigeria.