Ubiquitous in eukaryotes, Long Terminal Repeats (LTR) retrotransposons elements play important role in the genome evolution. Sequencing of genomes presents a great challenge of rapidly identifying them in large-scale genomic data. In this report we describe LTR_INSERT, a computational method for identifying LTR elements in genomic sequences. Our method provides structural and evolutionary supports to discover LTR elements. By applying LTR_INSERT to two rice genomes, we have identified 72 novel LTR families in the species of which LTR elements have been extensively mined.