A major goal of evolutionary biology is to understand the role of adaptive processes on sensory systems. Visual capabilities are strongly influenced by environmental and ecological conditions, and the evolutionary advantages of vision are manifest by its complexity and ubiquity throughout Metazoa. Crustaceans occupy a vast array of habitats and ecological niches, and are thus ideal taxa to investigate the evolution of visual systems. A comparative approach is taken here for efficient identification and classification of opsin genes, photoreceptive pigment proteins involved in color vision, focusing on two crustacean model organisms: Hyalella azteca and Daphnia pulex. Transcriptomes of both species were assembled de novo to elucidate the diversity and function of expressed opsins within a robust phylogenetic context. For this purpose, we developed a modified version of the Phylogenetically Informed Annotation tool’s pipeline to filter and identify visual genes from transcriptomes in a scalable and efficient manner. In addition, reference genomes of these species were used to validate our pipeline while characterizing the genomic architecture of the opsin genes. Next-generation sequencing and phylogenetics provide future venues for the study of sensory systems, adaptation, and evolution in model and nonmodel organisms.