In this study, homemade back-slopped yogurts were collected from seven different mountainous villages of Turkey and evaluated their microbiota via next-generation sequencing (NGS). The predominant taxa at the phyla level were Firmicutes (79.08–94.96%), Bacteriodetes (3.94–11.64%), and Proteobacteria (0.91–8.79%) which together accounted for more than 99% of the total relative bacterial abundance. Lactobacillus genus dominated the microbiota with 78.25% relative abundance followed by Streptococcus, Bacteroides, Prevotella, and Acinetobacter genera while Lactobacillus delbrueckii was the most prevalent species in yogurts except for TD3 and TD7 samples. Surprisingly, Lactobacillus helveticus species was present in large proportions in TD3 and TD5 samples with 61.20% and 36.70% relative abundances, respectively, however, it was not detected in TD1, TD4, and TD7. Besides, P. copri, B. vulgatus, F. prausnitzii, and B. dorei were amongst the most prevalent species in all samples. Overall, this study discussed the presence of B. vulgatus, F. prausnitzii, and B. dorei species which were previously recommended to be included in probiotic formulations and considered among the new generation probiotics and human health biomarkers in homemade yogurts besides main yogurt bacteria and L. helveticus. Therewithal, our work revealed crucial data related to the highly complex bacterial composition of homemade products through an NGS-based approach.