Mutant strains derived from Aspergillus niger C28B25 and belonging to series AW99 [producing maximum pectinase level in submerged fermentation (SmF)] and series AW96 [producing maximum pectinase level in solid-state fermentation (SSF)] were compared concerning morphological and pectinase properties. Study of the sporulation patterns on agar plates with glucose and deoxyglucose showed that AW99 mutants had a higher percentage of sporulated area than AW96 mutants and the wild strain. In addition, pectinases produced by the AW96-3 strain exhibited increased thermal stability compared to the pectinases produced by the AW99-iii strain either in SmF or SSF. Results support the idea that A. niger produces isoenzymes with differences in pectinase properties depending on the culture technique (SSF or SmF) and the strain used (wild type, AW96, or AW99). The results also suggest the presence of pleiotropic mutations of different kinds (AW96 and AW99) that simultaneously affect the sporulation and enzymological patterns of each class of mutants.