Mariner-like elements (MLEs) are ubiquitous DNA mobile elements found in almost all eukaryote genomes. Nevertheless most of the known copies are inactive and the question of the genome invasion by MLEs remains largely hypothetical. We have previously reported the presence of highly homologous copies of MLEs in the genome of phylogenetically distant crustacea living in the same hydrothermal environment suggesting the possibility of horizontal transfer. In order to further support the hypothesis that horizontal transmission of MLEs might occur between crustacean sympatric species, we described here 85 MLE sequences found in the genome of a large spectrum of coastal crab species. The number of the MLEs copies in genomes was variable. Half of these MLEs fit with the irritans subfamily of MLEs whereas the second half grouped in a new subfamily called marmoratus. In addition, a molecular phylogeny of crabs was established by using the 16S information. The comparison between 16S and MLEs based trees reveals their incongruence, and suggests either the existence of horizontal transfer events between phylogenetically distant species, or an ancestral MLE polymorphism followed by different evolution and stochastic loss.