The present study aimed to examine the presence of aflatoxin- and ochratoxin A (OTA)-producing fungi in dried chilli (Capsicum spp.). A total of 120 chilli samples, including 60 samples each of chilli powder and dried chilli pods, were examined for fungal contamination. Results showed that 86.7% and 96.7% of chilli powder and dried chilli pods, respectively, were contaminated by fungi at a concentration of <10³ CFU/g. Overall, 500 fungal isolates were recovered and identified using a morphological method. The most frequent strain was Aspergillus section Flavi (46.6%), followed by Aspergillus section Nigri (34%), Penicillium (7.6%), Aspergillus section Aspergillus (7.6%), Aspergillus section Circumdati (2.2%) and Rhizopus (2%). In total, 37.5% and 43.8% of Aspergillus section Flavi isolates obtained from dried chilli powder and dried chilli pods, respectively, produced aflatoxin. Of the 96 aflatoxigenic isolates, 96.9% of the strains produced aflatoxin B and 3.1% produced both aflatoxin B and G. However, β-tubulin sequence analysis revealed that all aflatoxin-producing isolates were identical to A. flavus. Moreover, 170 isolates of Aspergillus section Nigri, 11 of Aspergillus section Circumdati, 2 of Aspergillus section Flavi producing yellow-to-cinnamon colonies and 38 of Penicillium spp. were examined for their ability to produce OTA. In total, 1 isolate of Aspergillus section Nigri and 2 isolates of Aspergillus section Flavi produced OTA. The first isolate was identified as A. carbonarius, whereas the latter two isolates were both A. alliaceus. The highest OTA production by A. carbonarius (622.4 ng/g) was observed following incubation on MEA at 25 °C for 21 days. Conversely, the two A. alliaceus isolates produced OTA at levels of 583.7 and 743.7 ng/g, respectively, after cultivation on YES at 25 °C for 21 days. To the best of our knowledge, this is the first report regarding the natural occurrence of aflatoxin- and OTA-producing fungi in dried chilli from Thailand.