This study was performed to assess microbial contamination of Aronia melanocarpa, blueberry, raspberry, and cranberry sold in several markets. We investigated total aerobic bacteria and detected foodborne bacteria by multiplex PCR from Aronia melanocarpa, blueberry, raspberry, and cranberry. Total aerobic bacteria of each sample showed mean 3.54 log CFU/g for Aronia melanocarpa, mean 1.90 log CFU/g for blueberry, and mean 1.40 log CFU/g for raspberry, but not detected in cranberry. Specially, Aronia melanocarpa contained high total aerobic bacteria contamination among various berries and contamination level reached 4.17 log CFU/g in sample 5. To evaluate the effect of distribution conditions, we also investigated total aerobic bacteria of various berries. Total aerobic bacteria showed mean 2.89 log CFU/g for berries in refrigerated distribution and 1.40 log CFU/g in frozen distribution, but not in dry distribution. For assessment of foodborne bacteria contamination, we conducted PCR with multiplex primers of E. coli O157, S. aureus, B. cereus, V. parahaemolyticus, L. monocytogenes, Y. enterocolitica, Salmonella spp., Shigella spp. Among these foodborne bacteria, B. cereus was amplified in Aronia melanocarpa in sample 4 and blueberry in sample 1, 2, 3, and 5. The result of quantitative analysis of B. cereus contamination showed 4.08 log CFU/g of Aronia melanocarpa in sample 4 and higher contamination rate 4.07 log CFU/g of blueberry in sample 3. These results suggest that strict food safety control in harvest and distribution of various berries is necessary to prevent foodborne disease and improve microbiological safety.