Microbial contamination in dairy products, particularly cheese, significantly affects both product quality and safety. This study investigated the yeast and mold contamination in two types of cheese: Romi, a hard-ripened cheese, and Kariesh, a fresh soft cheese, providing insights into the microbial dynamics of different cheese varieties. Findings indicated that Kariesh cheese, due to its higher moisture content and favorable pH, exhibited significantly elevated yeast and mold counts compared to Romi cheese. The variability in microbial contamination in Kariesh was notably higher, highlighting its vulnerability to fungal growth, specifically Aspergillus flavus and niger. In contrast, Romi cheese, with lower moisture and higher salt content, showed more controlled contamination levels. PCR and sequencing confirmed the identity of fungal isolates, offering a molecular basis for understanding fungal diversity in these cheese types. Moreover, the study explored the inhibitory effect of Lactobacillus plantarum on fungal growth, with higher concentrations (9 Log₁₀ cfu/g) showing more significant inhibition of both A. flavus and A. niger. However, the antifungal activity diminished over time, suggesting a need for combining probiotics with other preservation methods. These findings underline the importance of optimizing preservation strategies in soft cheeses like Kariesh to extend shelf life and ensure safety.