The objective of this study was to isolate and identify molds in processed, kareish, and ras (roumy) cheese samples obtained from Kafrelshiekh city, Egypt. Additionally, the study aimed to conduct trials to control mold growth and measure the levels of aflatoxin M1 and ochratoxin A in some cheese samples. Out of 60 randomly selected samples, 31 (51.67%) were found to be positive for the presence of various mold species, with frequencies of 45%, 55%, and 55% in processed, kareish, and ras cheese samples, respectively. The mean mold counts were 2.51 ± 1.90 cfu/g, 3.42 ± 2.48 cfu/g, and 2.59 ± 1.79 cfu/g (log 10), respectively. Several mold species were identified in the positive samples, including Penicillium spp., Aspergillus spp., Mucor spp., Alternaria spp., Fusarium spp., Geotrichum candidum, Chrysonilia sitophila, and Endomyces fibuligera. PCR analysis and the detection of aflatoxin regulatory genes (aflR, Ver1, Nor1, and omtA) were employed to assess the afla-toxigenicity of three Aspergillus flavus isolates. All three isolates tested positive for the aflR and Ver1 genes; one isolate was positive for the omtA gene, while the Nor1 gene was not detected in any of the three isolates. Additionally, three Aspergillus niger isolates were tested for ochratoxin production using PCR to identify the Pks gene, revealing that the Pks gene was present in two of the isolates. The levels of AFM1 and ochratoxin A in the cheese samples under examination were found to be below the permitted limits outlined by ISO 14675 and EC 1881, respectively. Furthermore, the findings demonstrate that natamycin (0.015%) combined with thyme oil (2%) effectively inhibited the growth of A. flavus and A. niger in vitro, indicating their potential use in cheese production to prevent mold growth and the associated economic losses during storage.