While the study of transposable element evolution has been conducted in several model insect organisms such as Anopheles gambiae, Drosophila melanogaster, and Bombyx mori, little investigation has been conducted into the transposable element (TE) evolution within less commonly examined model and non-model taxa within Diptera. In this work we contributed two analyses to close this gap. First, TEs in the lepidopteran, Heliconius melpomene, were characterized, and it was determined that 25% of the genome is composed of TEs. Second, TEs in oestroid and muscid flies were characterized using survey sequencing rather than whole genomes. Comparative analyses were performed on Haematobia irritans, Sarcophaga crassipalpis, Phormia regina, and Cochliomyia hominivorax. TE proportions were 5.95%, 10.00%, 22.43%, and 30.67%, for C. hominivorax, P. regina, S. crassipalpis and H. irritans, respectively. These studies provide new insights into the diversity of TEs in Insecta and suggest that in general, TE diversity is high among insects.