Emerald ash borer (EAB, Agrilus planipennis), an exotic invasive pest, has killed millions of ash trees (Fraxinus spp.) in North America and continues to threaten the very survival of the entire Fraxinus genus. Despite its high-impact status, to date very little knowledge exists for this devastating insect pest at the molecular level. Mariner-like elements (MLEs) are transposable elements, which are ubiquitous in occurrence in insects and other invertebrates. Because of their low specificity and broad host range, they can be used for epitope-tagging, gene mapping, and in vitro mutagenesis. The majority of the known MLEs are inactive due to in-frame shifts and stop codons within the open reading frame (ORF). We report on the cloning and characterization of two MLEs in A. planipennis genome (Apmar1 and Apmar2). Southern analysis indicated a very high copy number for Apmar1 and a moderate copy number for Apmar2. Phylogenetic analysis revealed that both elements belong to the irritans subfamily. Based on the high copy number for Apmar1, the full-length sequence was obtained using degenerate primers designed to the inverted terminal repeat (ITR) sequences of irritans MLEs. The recovered nucleotide sequence for Apmar1 consisted of 1,292 bases with perfect ITRs, and an ORF of 1,050 bases encoding a putative transposase of 349 amino acids. The deduced amino acid sequence of Apmar1 contained the conserved regions of mariner transposases including WVPHEL and YSPDLAP, and the D,D(34)D motif. Both Apmar1 and Apmar2 could represent useful genetic tools and provide insights on EAB adaptation.