Anemonefish consists of 30 species and are likely the most recognizable fishes to the public due to their unique colour patterns, easy captive breeding, and the animation film Finding Nemo. They are also important species to biologists owing to their symbiotic relationship with anemones as well as sequential hermaphroditism and hence serve as emerging model organisms in ecology, evolution, and development. The latest advancements in high-throughput sequencing technologies and bioinformatic analysis have facilitated studies in anemonefish research. In this chapter, we first show the recent genomics studies that unveil the genomic architecture and underlying evolutionary processes in anemonefish. We also cover how state-of-the-art transcriptomic and proteomic techniques have been utilized to capture and uncover the fundamental molecular mechanisms driving dynamic changes in biological processes throughout development and under various environmental changes.