The genomic dataset consists of 373 bacterial strains spanning 3 phyla (172 Actinomycetota, 6 Bacillota and 195 Pseudomonadota), 17 genera and 47 species, isolated from French PDO cheeses and milks or issued from private and international bacterial culture collection. Complete genome sequences were generated using short-read DNA sequencing technology (Illumina NovaSeq 6000). For 37 strains, long-read DNA sequencing technology (Oxford Nanopore PromethION) was used in combination with Illumina sequencing.