Streptococcus salivarius is a bacterial species that belongs to microbiomes of all humans and contributes to the maintenance of oral, pharyngeal and gut health. The high genomic diversity observed in this species is mainly caused by horizontal gene transfer. This work aimed to evaluate the contribution of integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) in S. salivarius genome diversity. For this purpose, we performed in-depth analysis of 75 genomes of S. salivarius and searched for signature genes of conjugative and mobilizable elements. This analysis led to the retrieval of 69 ICEs, 165 IMEs and many decayed elements showing their high prevalence in S. salivarius genomes. The exhaustive analysis of the adaptation genes carried by these elements showed that they encode numerous functions including resistance to antibiotics. The ICEs and IMEs detected in this commensal species belong to the same families of elements than other elements described in pathogenic streptococci (Streptococcus agalactiae, Streptococcus suis) and other Firmicutes. These mobile genetic elements can thus participate to antibiotic resistance dissemination between various species.