Technical Abstract: The integration of transposable elements within gene coding regions can affect expression levels and transcript splicing patterns. The repetitive element, Lep1, is comprised of a conserved 134 base pairs (bp) consensus core region among species of Lepidoptera, and was defined as a short intersperse nuclear element based upon structural features including a transfer-ribonucleic acid-derived region, an internal ribonucleic acid polymerase III promoter preceded by a promoter element, and a 3' flanking poly-thymidine termination signal. Lep1 elements also contain an internal microsatellite that was mobilized within transcripts under cell stress conditions, and reintegrated into the genome by reverse transcription. In total, 5541 Lep1 copies were predicted within the silkmoth, Bombyx mori, whole genome assembly, shown to be localized with gene coding regions, and integration into transcribed regions documented through annotation of chimeric expressed sequence tags from species of Lepidoptera. Lep1 short intersperse nuclear elements are actively mobile within genomes and are a source of haplotype variation within gene coding regions, but the impact on gene expression, transcript splicing, or resultant function within species of Lepidoptera remains unknown.