The main purpose of this study was to degrade total petroleum hydrocarbons (TPHs) from contaminated soil in batch microcosm reactors. Native soil fungi isolated from the same petroleum-polluted soil and ligninolytic fungal strains were screened and applied in the treatment of soil-contaminated microcosms in aerobic conditions. The bioaugmentation processes were carried out using selected hydrocarbonoclastic fungal strains in mono or co-cultures. Results demonstrated the petroleum-degrading potential of six fungal isolates, namely KBR1 and KBR8 (indigenous) and KBR1-1, KB4, KB2 and LB3 (exogenous). Based on the molecular and phylogenetic analysis, KBR1 and KB8 were identified asAspergillus niger[MW699896] andtubingensis[MW699895], while KBR1-1, KB4, KB2 and LB3 were affiliated with the generaSyncephalastrumsp. [MZ817958],Paecilomyces formosus[MW699897],Fusarium chlamydosporum[MZ817957] andConiochaetasp. [MW699893], respectively. The highest rate of TPH degradation was recorded in soil microcosm treatments (SMT) after 60 days by inoculation withPaecilomyces formosus97 ± 2.54%, followed by bioaugmentation with the native strainAspergillus niger(92 ± 1.83%) and then by the fungal consortium (84 ± 2.21%). The statistical analysis of the results showed significant differences.