This study aims to select fungi isolates to reduce olive mill wastewater (OMWW) chemical oxygen demand (COD) and phenolic compounds (PC), as well as their genotoxicity effect. Treatment with mold, isolated by an innovative technique using phenolic compound-selective media, showed a reduction rate of about 4% for COD and 2% for PC during one month of incubation without optimization of the treatment conditions. Whereas this percentage reached 98% and 96% for COD and PC, respectively, after only 12 days of treatment, when the C:N ratio was adjusted to 30 by adding urea as a nitrogen source at 150 rpm agitation speed. Genetic sequence homology of the most efficient mold isolate showed 100% similarity to Penicillium chrysogenum. High-performance liquid chromatography analysis of phenolic extracts of untreated OMWW showed the presence of five compounds—hydroxytyrosol at 1.22 g.L⁻¹, tyrosol at 0.05 g.L⁻¹, caffeic acid at 0.16 g.L⁻¹, p-coumaric acid at 0.05 g.L⁻¹ and oleuropein at 0.04 g.L⁻¹—that were eliminated during the degradation process at 88.82%. Genotoxicity, assessed by the Vicia-faba root cell, showed a significant decrease in micronucleus frequency of about 96% after fungal treatment. These results confirm the positive role of fungal treatment of OMWW to eliminate genotoxicity and their ability to improve the agronomic potential.