Bougainvillia cf. muscus is an operational taxonomic unit (OTU) representing a coastal hydrozoan (family Bougainvilliidae) closely resembling the highly polymorphic species Bougainvillia muscus. This marine invertebrate exhibits a dimorphic life cycle characterized by a sessile, branching colonial hydroid stage and a planktonic, sexually reproducing medusa stage. The hydroid colony forms irregular, tree-like or bushy tufts up to 120 mm in height, bearing fusiform hydranths with 10–18 tentacles surrounding a conical hypostome. The free-swimming medusa is distinguished by a cubic umbrella, branching oral tentacles, and four prominent marginal bulbs, each uniquely bearing approximately seven simple eyes (ocelli). Recently highlighted in evolutionary biology, the complete genome of Bougainvillia cf. muscus has been sequenced and assembled into a high-quality 375 Mb genome. This genomic dataset features thousands of predicted protein-coding genes and high macrosynteny with other hydrozoans, serving as a pivotal reference for investigating the molecular evolution of vision-related genes and early metazoan sensory systems.