The use of advanced bacterial identification tools such as sequencing the bacterial genome allows a complete understanding of the bacterial ecology of artisanal salami. Thus, the objective of this work was to evaluate the complete microbiota in artisanal salami, through the use of genetic sequencing. For this, the identification of bacteria in artisanal salami was performed on days 0, 14, and 28 days of fermentation using high performance sequencing of the V3/V4 regions of the 16S rRNA gene using primers 341F (CCTACGGGRSGCAGCAG), and 806R (GGACTACHVGGGTWTCTAAT ), with 300 cycles and single-end sequencing (MiSeq Sequencing System equipment, Illumina Inc., USA). A total of 197 genera and 572 species of bacteria were found throughout the fermentation. The genera Acinetobacter (13%), Enterobacter (10%), Enterococcus (9%), and Bacillus (9%) were more abundant on day 0. Enterococcus casseliflavus (8%), Enterobacter cloacae (6%), Acinetobacter baumannii (6%), Wautersiella falsenii (6%) also stood out. These species represent the processing conditions of the salami, suggesting possible contamination at the beginning of the production process. On day 14 of fermentation the predominat genera were Acinetobacter (20%), Enterobacter (18%), Citrobacter (17%), Aeromonas (10%) and Companilactobacillus (8%), in addition to the species Citrobacter freundii (18%), Enterobacter aerogenes (13%), Companilactobacillus farciminis (10%) and Enterobacter cloacae (9%). C. freundii, E. aerogenes, and E. cloacae could produce undesirable biogenic amines. A C. farciminis species also stood out as a lactic acid bacterium allowing the stablishment of the fermentative process. On day 28, Companilactobacillus spp. (10%) and Staphylococcus spp. (64%) as well as the species C. farciminis (10%) and S. saprophyticus (63%) show greater abundance, and are characterized by the high acidification rate of the product inhibiting the development of undesirable bacteria at the ending of the fermentation process. Thus, the species C. farciminis can potentially be applied as a starter culture in salami.