Convergently evolved traits act like replicates in the singular history of life, allowing biologists to ask whether evolution follows similar or different paths to similar end points. One such trait is animal eyes, which evolved convergently numerous times, and therefore could allow biologists to understand whether evolution took similar genetic paths to evolving eyes repeatedly. However, beyond a few specific candidate genes, not much work has been done investigating convergence versus divergence of genes expressed in convergently evolved eyes. This research is important because it can parse the roles of gene duplications, protein coding mutations, gene regulation, and co-option in convergent evolution. A unique group in which to study convergent evolution is Cnidaria because eyes evolved convergently multiple times within Medusozoa (jellyfish). Furthermore, eyes are an excellent trait for studying genetic evolution because scientists know a lot about genetic mechanisms like phototransduction, especially in model systems. We used genomics and transcriptomics to characterize the molecular evolution and expression of candidate phototransduction genes in three cnidarian species: Hydra vulgaris, which lack eyes but exhibit light-dependent behavior, and two species with convergently evolved eyes Tripedalia cystophora and Aurelia aurita. Results from this study show that while many homologous genes annotated with phototransduction functions are upregulated in the eyes, many components vary by eye origin. Therefore, despite common claims in evo-devo for master regulatory genes and deep homology, we find many genes to be specific to convergently evolved eyes, indicating that evolution may often take different paths to similar end points.