The transposase of the mariner-like elements (MLEs) specifically binds as a dimer to the inverted terminal repeat of the transposon that encodes it. Two binding-motifs located within the inverted terminal sequences (ITR) are therefore recognized, as previously indicated, by biochemical data obtained with the Mos1 and Himar1 transposases. Here, we define the motifs that are involved in the binding of a MLE transposase to its ITR by analyzing the nucleic acid properties of the 5' and 3' ITR sequences from 45 MLEs, taking into account the fact that the transposase binds to the ITR, using its CRO binding domains and the general characteristics of the cro binding sites so far investigated. Our findings show that in all the MLE ITRs, the outer half was better conserved than the inner half. More interestingly, they allowed us to characterize conserved palindromic and mirror motifs specific to each "MLE species". The presence of the palindromic motifs was correlated to the binding of the transposase dimer, whereas the properties of the mirror motifs were shown to be responsible for the bend in each ITR that helps to stabilize transposase-ITR interactions.