Evolution produces new traits by tinkering with existing genes or through the emergence of de novo genes. Comparative genomics data can be used to explore the interplay between gene recruitment and de novo gene birth during the evolution of novel traits. We focus our studies on the Batrachoididae, commonly known as toadfishes, an diverse family of ray-finned fishes with an arsenal of derived traits such as venom, bioluminescence, and acoustic signaling. Although acoustic signaling is shared across the family, not all toadfishes are venomous or bioluminescent. Currently, there are representative genomes for three out of the four Batrachoididae subfamilies. To complete the genomic sampling across all subfamilies, we sequenced the genome of a bioluminescent toadfish, Porichthys myriaster, using Illumina and Oxford Nanopore technologies. We produced a hybrid de novo assembly consisting of 10,949 scaffolds containing 87% core Actinopterygii genes and 29,929 proteins. With this assembly in hand, we aimed to (1) investigate the evolution of natterins, a class of proteins found in toadfish venom, and (2) identify novel or duplicated gene families unique to luminous toadfishes. We identified several natterin homologs and candidate protein homologs for a novel crystallin previously reported in the lens of Porichthys’s light organs. Our crystallin candidates are functionally uncharacterized and similar proteins are found only in other fishes, fungi, and bacteria. Comparative analyses across toadfish genomes are underway, and we anticipate that our approach will identify conserved and novel genomic features useful for understanding the diversity of genetic mechanisms associated with phenotypic evolution.