During sub-culturing on solid media, the colonies of filamentous fungi frequently degenerate with the loss of conidiation, pigmentation, and reduction or loss of production of secondary metabolites. The degenerated cultures of three fungal species, i.e., Aspergillus nidulans, Cordyceps militaris and Metarhizium robertsii were obtained from the spontaneous colony sectors showing the typical non-sporulation features. To determine the presence of if any genetic mutations, we extracted the DNA from the degenerated cultures of these three fungi for genome re-sequencing with the Illumina technique.