Target spot, caused by Corynespora cassiicola, is a common lower canopy disease of soybean in the southern United States. Given the recent resurgence of target spot and increasing reports of resistance to the quinone outside inhibitor (QoI) fungicide class within C. cassiicola, a survey of C. cassiicola from the Mississippi soybean production system was initiated in 2019 to determine the nature of its resistance mechanisms. A total of 819 monoconidial isolates were collected from 228 geographic field locations in 75 Mississippi counties. The molecular mechanism of resistance was determined using a PCR-RFLP analysis by comparing nucleotide sequences in the cytochrome b gene. The percentage of isolates containing the G143A substitution increased from 71.3% in 2016 to 93.5% in 2021. In all, 85.8% of the C. cassiicola isolates carried the G143A substitution. The EC50 values of QoI-resistant and -sensitive isolates to azoxystrobin varied significantly with QoI-sensitive isolates exhibiting lower EC50 values than QoI-resistant isolates. Moreover, results of fitness evaluations indicated that QoI-resistant isolates are more competitive than QoI-sensitive isolates and there were no fitness costs associated with QoI resistance in C. cassiicola. Additionally, the sensitivity of six C. cassiicola isolates to eight fungicide active ingredients in four fungicide classes were evaluated. Results indicated that three succinate dehydrogenase inhibitors benzovindiflupyr, fluxapyroxad, and pydiflumetofen were the most effective in inhibiting mycelial growth regardless of isolate phenotype followed by the methyl benzimidazole carbamate thiophanate-methyl, two demethylation inhibitors (DMI) difenoconazole and flutriafol, the QoI pyraclostrobin, and the DMI prothioconazole. Furthermore, the efficacy of seven commercial fungicides on target spot was evaluated in the greenhouse and field. Pydiflumetofen + difenoconazole, fluxapyroxad + pyraclostrobin, and thiophanate-methyl delayed disease progress and protected soybean yield, which indicated their effectiveness in managing target spot. Pydiflumetofen + difenoconazole also significantly reduced defoliation. Notably, fungicides applied at R3 were more effective in reducing disease severity and defoliation than additional growth stage timings. The current study revealed a reduction in C. cassiicola sensitivity to QoI fungicides and a shift to QoI-resistant populations exhibiting fitness advantages. Our findings provide pertinent information for growers as to which fungicides should be recommended to manage target spot.