The Crown-of-Thorns starfish Acanthaster planci are corallivorous starfish known for significant population density variations throughout their tropical Indo-Pacific geographical range. During periods of population outbreaks they can significantly reduce coral cover on infested reefs. Reef monitoring data spanning some 30 years on the Great Barrier Reef of Australia has revealed that Crown-of-thorns starfish account for 42% of coral loss and is the single most important factor impacting reefs after cyclones. An understanding of A. planci developmental biology may offer insights into key embryonic and larval processes and reveal avenues by which this species may be manipulated to help mitigate the damage these starfish causes to the coral reef. As a first step towards linking ecological data and echinoderm developmental biology, we sequenced the A. planci genome and identified a Hox and ParaHox cluster.