The dairy industry is constantly developing new starters with specific traits. Therefore, strains from natural sources have huge potential for exploration and characterization. The aim of this work was to identify the most efficient, useful, and reliable option for typing 55 Streptococcus thermophilus isolates from traditional Turkish yogurts and four industrial strains. Then, we statistically evaluated whether our conclusions could be extended to the true population. For this purpose, the results of the rapid amplified polymorphic DNA polymerase chain reaction (RAPD-PCR; using the OPI-02 MOD, M13, and XD9 primers) and pulsed-field gel electrophoresis (PFGE; using the SmaI and ApaI enzymes) typing methods were compared. The discriminatory power, typeability, and reproducibility were analyzed. Additionally, the congruence between typing methods was quantified using the adjusted Rand index (AR), Wallace index (W), and expected Wallace coefficient. Both methods revealed high genetic diversity of the S. thermophilus strains, even in the same yogurt sample. The numerical combination of results for these primers or restriction enzymes increased the congruence between the methods and provided more complete information on the strains. The comparison of these two options showed that using SmaI with ApaI was more advisable and useful than using OPI-02 MOD with M13. Additionally, the first combination represented the best tool to discriminate S. thermophilus strains (Simpson's index of diversity [DI] of 0.999 [0.997-1.000]). This finding was statistically supported. The RAPD (OPI-02 MOD) typing result showed an ability to confidently predict the PFGE (SmaI, ApaI) type (AR = 0.782 [0.618-0.949], W = 0.946 [0.865-1.000]). This result had some statistical support and might represent an important application in the dairy industry for screening strains.