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Spices are widely used in various cuisines in Malaysia to enhance the flavour and aroma. However, spices are susceptible to fungal infection, leading to mycotoxin contamination if the storage conditions are favourable for fungal growth. Thus, this study aimed to identify fungal species in spices commonly used in local Malaysian cuisines and determine their prevalence and mycotoxigenic potential. A total of 110 spice samples consisting of cumin, fennel, coriander, peppers (black pepper and white pepper), chillies (dried chilli, chilli paste and chilli powder), cinnamon, star anise, cloves, curry powder and korma powder were randomly purchased from retail markets in Penang. The samples were analysed for the total fungal count (ground spices) and the incidence of fungal infection (whole spices). The fungal species isolated from spices were identified based on morphological and molecular approaches, and the mycotoxigenic potential was determined using the Coconut Cream Agar method. The results showed that coriander seeds (ground) recorded the highest total fungal count (ADM 3.08 log CFU/g; DG18 3.14 log CFU/g), while black pepper (whole) recorded the highest incidence of fungal infection (94%). Interestingly, star anise and cloves were free from fungal contamination. The mycotoxigenic fungi of A. flavus and A. niger recorded the highest isolation frequency in ground and whole spices. These findings indicate the risk of mycotoxin exposure to consumers due to the high consumption of spices in local Malaysian cuisine.