Red pepper is a spice vulnerable to fungal growth and mycotoxin contamination while in the field and post-harvest during storage. Storage fungi are omnipresent and colonize fast when moisture levels go up, ultimately leading to mycotoxin production. Stored samples of the whole, crushed and ground red pepper in the Southern Indian States and Maharashtra, India were examined to isolate and characterize the prevalent contaminant fungal species. The average moisture content was below 10% for all the red pepper samples and the average total fungal load was less than 1×10⁴ CFU/g. Crushed red pepper showed higher fungal counts than ground and whole red pepper. The identified contaminant mycoflora belonged to the group; Aspergillus, Eurotium sp., Cladosporium sp., Eupenicillium sp., Penicillium sp., Miscellaneous fungi, Neosartorya sp., Curvularia sp., and Hyphopichia sp. Aflatoxigenic Aspergillus flavus was present only in 8.3% of the crushed and 2.54% of whole red pepper samples stored for more than two months.