Bozcaada which is a province of Canakkale, Turkey, is located between the 39 degrees 48 north parallel and 26 degrees east meridians. The largest livelihood of Bozcaada is viticulture. Therefore, in our study, microbial load, and mould diversity of the Cavus (table) and Karalahna (wine) grapes which are endemic to the island were evaluated, and ochratoxin production potentials of Aspergillus isolates were investigated by HPLC. A total of 6 vineyards with Cavus and Karalahna grapes were sampled in 2015 and 2016. Total aerobic mesophilic bacteria count of grapes ranged between 0.00 and 4.21 log CFU/g, yeast load between 0.00 and 2.66 log CFU/ g and mould load between 1.67 and 3.20 log CFU/g. A total of 2264 mould isolates were taken from samples. All isolates were identified at the genus level. Aspergillus spp. and Penicillium spp. were the most isolated species in 2015, while Alternaria spp. and Cladosporium spp. were the most isolated species in 2016. It was determined that 13.78% (312) of the isolates were Aspergillus spp., 54 of these isolates, have been selected and identified at the species level. Twenty-one of the black Aspergillus isolates were identified as A. niger / A. acidus, twenty-four of them were A. carbonarius and one of them is A. ibericus. The two white isolates were found to be A. candidus, the creamy brownish-spore forming isolate was A. terreus, and three green isolates were identified as A. flavus, A. calidoustus and A. sydowii. Six isolates (4 A. niger, 1 A. calidoustus, and 1 A. sydowii) were producing OTA. The amounts of ochratoxins varied from 0.80 to 74.01 ng/g.