Abstract Samples of cheeses naturally contaminated with moulds (12 samples of mouldy Manchego cheese and 10 of a naturally ripened blue cheese) were analysed for the presence of mycotoxins (aflatoxins BI and MI, sterigmatocystin, patulin, penicillic acid and mycophenolic acid in Manchego cheese, and mycophenolic acid and roquefortine in blue cheese). In addition, 24 Penicillium and Aspergillus strains isolated from the samples were assessed for their mycotoxigenicity. Four of Manchego cheese samples were positive to mycophenolic acid and one sample of blue cheese contained roquefortine. The rest of mycotoxins investigated were not found. One Aspergillus strain isolated from Manchego cheese showed the ability to produce aflatoxin MI. The rest of strains from these samples being no producers. In contrast, 7 out of 9 Penicillium ( P. roqueforti) strains isolated from blue cheese were able to produce roquefortine, with one strain also producing mycophenolic acid.