Orthorhombic (spherical; similar to 10 nm) and monoclinic (cylindrical; similar to 50 nm) sulfur nanoparticles (SNPs) were synthesized and examined for their effects on the total lipid content and desaturase enzymes of Aspergillus niger. Synthesized SNPs were characterized for size with transmission electron microscopy, elemental composition with energy dispersive X-ray spectroscopy and allotropic nature with X-ray diffraction pattern. Both the SNPs considerably reduced total lipid content of the treated fungal isolates with significant down regulation of the expression of various desaturase enzymes (linoleoyl-CoA desaturase, stearoyl-CoA 9-desaturase and phosphatidylcholine desaturase). Unusual high accumulation of saturated fatty acids with depleted lipid layer can be inferred as one of the major reasons of SNPs mediated fungistasis.