Tyrosine-based site-specific recombinases (TBSSRs) are DNA breaking-rejoining enzymes, which in bacterial genomes play a major role in the comings and goings of mobile genetic elements (MGEs), but also in the segregation of plasmids and chromosomes, the resolution of plasmid dimers and of co-integrates resulting from the replicative transposition of transposons. With the aim of improving the annotation of TBSSR genes in genomic sequences and databases, which so far is far from robust, we built a set of over 1300 TBSSR protein sequences tagged with their genome of origin. We organized them in families to investigate i) whether TBSSRs tend to be more conserved within than between classes of MGE types and ii) whether the (sub)families may help in understanding more about the function of TBSSRs associated in tandem or trios, found on plasmids and chromosomes. 67% of the TBSSRs in our set are MGE type specific. The simple in silico procedure described here could contribute to greatly improve the annotation of tyrosine-based site-specific recombinases belonging to well characterized types of MGEs. It also reveals TBSSRs families belonging to genetic entities that by their distribution among bacterial taxa, seem to contribute to lateral gene transfer.