Representatives of five distinct types of transposable elements of the mariner family were detected in the genomes of the Queensland fruit fly Bactrocera tryoni and its sibling species Bactrocera neohumeralis by phylogenetic analysis of transposase gene fragments. Three mariner types were also found in an additional tephritid, Bactrocera jarvisi. Using genomic library screening and inverse PCR, full-length elements representing the mellifera subfamily (B. tryoni.mar1) and the irritans subfamily (B. tryoni.mar2) were isolated from the B. tryoni genome. Nucleotide consensus sequences for each type were derived from multiple defective copies. Predicted transposase sequences share approximately 23% amino acid identity. B. tryoni.mar1 elements have an estimated copy number of about 900 in the B. tryoni genome, whereas B. tryoni.mar2 element types appear to be present in low copy number.