Comparative typing analysis of 25 Lactobacillus delbrueckii subsp. bulgaricus strains, isolated from traditional yoghurts in Turkey, was performed by RAPD-PCR (randomly amplified polymorphic DNA-PCR) and MLST (multilocus sequence typing). RAPD-PCR analyses were performed using two primers; M13 and 1254. Primer 1254 produced better results than primer M13. The bands produced by primer 1254 were brighter and easier to interpret, and a higher number of bands were produced. In addition, clusters produced by primer 1254 were grouped according to the source of isolation. MLST analysis was performed using three genes, beta-gal, pheS and rpoA, and isolates were successfully characterized at strain level. To our knowledge, MLST analyses were used for the first time for strain level discrimination in L. delbrueckii subsp. bulgaricus. It enabled a detailed understanding of L. delbrueckii subsp. bulgaricus strains by using allele and sequence types' analysis. Both MLST and RAPD allowed for the typing of clusters according to the isolation source, while RAPD provided an increased differentiation. However, by increasing the number of genes analyzed, the discriminatory power of MLST could be increased.