This study examines the evolution of Litobothrium aenigmaticum, a bizarre tapeworm that parasitizes pelagic thresher sharks in Taiwan and Mexico. Although this species nests robustly within the genus Litobothrium, it lacks all the characteristics typically displayed by this group. Furthermore, transmission electron microscopy has revealed that the attachment organ of this worm contains 11 unique cell types that have not been seen in any other tapeworm species. Our current study investigates the mechanisms that may have allowed for the evolution of this unusual morphology using comparative genomics and transcriptomics. To this end, we have assembled and annotated the genome of three litobothriidean species: L. aenigmaticum, its sister taxa L. daileyi, and the more distantly related L. amplifica. The genomes for these species range in size from 300–320 Mb with approximately 19,045–27,953 genes. Gene family evolution is currently being assessed with the program CAFE. Transcriptomes have also been generated for the three litobothriidean species. Differential gene expression analyses do not show many differences in gene expression, however, there appear to be some modest differences in the expression levels of genes associated with the immune system and anatomical structure. Overall, our current results indicate that the change in morphology may be due more to genomic change than differences in gene expression.