In order to preserve the traditional manufacturing of white pickled (WPC) and fresh soft cheeses (FSC), well-characterized autochthonous lactic acid bacteria (LAB) with advantageous characteristics were applied for the production of the cheeses at small industrial scale under the controlled conditions. Selected LAB for design of defined mixed starter cultures belonged to Lactococcus lactis ZGBP5-9, Enterococcus faecium ZGPR1-54 and Lactobacillus plantarum ZGPR2-25 for FSC production and to Lc. lactis BGAL1-4, Lactobacillus brevis BGGO7-28 and Lb. plantarum BGGO7-29 for WPC production. A sensory evaluation indicated that the cheeses obtained by inoculation with selected autochthonous LAB are similar to the traditional cheese and received the best scores. Viable cell counts of LAB used for the production of both type chesses was high, over 106 cfu g1. High viability of the surveyed strains was supported with PCR-DGGE, which confirm the retention of selected LAB strains as starter cultures in cheese production. Next, PFGE analysis showed that each single strains, selected in particular cheese mixed culture, revealed unique SmaI PFGE pattern that could enable efficient discrimination and monitoring of the strains in industrial process. As some of the selected LAB strains are attributed as potential probiotics, produced cheeses could be considered as functional food.