Lactic acid bacteria (LAB) diversity associated with tocosh, Peruvian traditional fermented potatoes, was for the first time investigated by culturing and high throughput sequencing (HTS) approaches. They were applied on three samples i.e. freshly harvested potatoes, one-month and eight-months production. While by culture-dependent approach a few Lactobacillus (Lb) species (Lb. sakei, Lb. casei, Lb. farciminis, Lb. brevis, Lb. fermentum) and Leuconostoc (Ln) mesenteroides were identified, twenty-four OTUs belonging to six LAB genera were considered in tocosh samples by HTS, being Lactobacillus dominant in all three samples. LAB predominated on fresh potatoes, while Clostridium, Zymophilus and Prevotella were the most abundant genus in 1- and 8-months tocosh samples. When biotechnological features were investigated, amylase and phytate-degrading abilities as well as EPS and group B vitamin (riboflavin and folate) production were exhibited by several Lb. sakei and Ln. mesenteroides strains. Safety traits of major LAB species from tocosh showed antibacterial activities as well as biogenic amines production capacity. The molecular inventory achieved by HTS approach provided information on LAB population composition during fermentation of this ancestral potato fermented product while culturing allowed the selection of LAB strains suitable for novel functional cultures design for the production of fermented starchy products.