Numerous genomes are available in databases and one of the biggest challenges is to understand the function of each gene. In bacteria, transposon mutant libraries have long been used to identify genes important for bacterial survival, growth or virulence. These methods have been very useful but time consuming as they relied on the analyses of individually isolated mutants. Moreover, they did not allow an exhaustive study of the bacterial genome. Recent advances in high throughput sequencing now allow the screening of millions of mutants in a single or few experiments using methods such as TraDIS or Tn-seq. These methods are sensitive enough to detect small defects in mutant fitness and allow the study not only of genes but also intergenic regions, promoter regions and essential protein domains in coding sequences if the library is saturated with transposon insertions. Here, we present the construction and the characterization of two saturated libraries in Salmonella Typhimurium ATCC 14028 and S. Enteritidis LA5 virulent strains, which are commonly used in research laboratories. Those libraries have been obtained using the Himar1 transposon that randomly inserts into TA dinucleotides sites on the genome. Those sites are present throughout the genome and there are few hot spots at the pathogenicity islands that have a lower GC%. Insertion of the transposon was obtained by conjugation between an E. coli donor strain harboring the plasmid pSAM_Ec (Kanamycin Himar transposon) and the Salmonella strain of interest. Transposon mutant libraries were sequenced with an Illumina NextSeq 500 using a read length of 75 bp. After read mapping, further analyses were carried out with the TRANSIT software that uses a Bayesian method based on the length of sequences containing TA sites without insertion completed with a Hidden Markov Model (HMM), which considers local differences in the read counts. These analyses confirmed the saturation of the transposon mutant libraries both on the chromosome and on the virulence plasmid and allowed us to to determine for each serovar the essential genes and the genes providing advantage or disadvantage for bacterial growth. These Tn-seq libraries are now used in several research projects and are available to the scientific community through collaboration.