To date, edible fungi such as black Aspergillus (Aspergillus niger aggregates) have been considered as safe. However, it has recently been reported that some strains have a mycotoxin biosynthetic capability, and this capability must be evaluated to determine the safety of edible fungi. In this study, we assessed the ability of mycotoxin production in A. niger aggregates isolated from various Korean foods using multiplex PCR and high-performance liquid chromatography (HPLC) analyses. Multiplex PCR and HPLC analyses of 32 A. niger aggregates showed that ochratoxin and fumonisin were produced only by strains exhibiting positive PCR patterns with ochratoxin and fumonisin biosynthesis genes. However, several strains did not produce mycotoxins, even though they contained mycotoxin biosynthesis genes. Using multiplex PCR pattern and HPLC analyses, we selected Aspergillus strains that do not produce mycotoxins, which will contribute to the development of safer fermented foods.