Although parasitism is often associated with a reduction in eye structures, the evolutionary processes driving this reduction are not well-known. Bat flies, a group of parasitic species evolved from fully visual, free-living ancestors, are a unique study system to address this due to the varying levels of eye reduction observed throughout the clade, including species with complete eye loss. The variation in bat fly eye micromorphology (0-54 facets) may also reflect microstructural changes associated with low light levels such as rhabdomere rearrangements. In order to investigate changes in the molecular components associated with these anatomical changes, we assembled de novo transcriptomes (8 spp.) and de novo genomes from (5 spp.) from a diversity of bat fly species. These assemblies were annotated for opsin genes, which encode proteins that are responsible for light detection. Thus far, our analyses of transcriptomes reveal that a common dipteran rhodopsin, Rh1, is present in most bat fly species, with the additional Rh6 present in Basilia species. Multi-level analysis using both transcriptomes and genomes allows for confirmation of sequences and a more comprehensive understanding of the RNA expression levels contributing to genetic changes. This work aims to elucidate the evolutionary trajectories of broader ectoparasite trends in visual system reductions.