Abstract A key strategy to reduce coral loss is the development of effective control method for the corallivorous crown‐of‐thorns sea star ( Acanthaster planci ), an omnipresent scourge and threat to the biodiversity of reefs in the Indo‐Pacific region. Limited genetic resources are available for this highly fecund species. In this study, we explored one aspect at the heart of A. planci outbreaks, the male reproductive system. Using high‐throughput sequencing technology, we report for first time the production of a comprehensive transcriptomic data set for the testes of A. placni that can aid in understanding the molecular mechanisms involved in A. planci spermatogenesis and fertilization. Through de novo transcriptome sequencing, we produced 52 965 998 raw reads corresponding to 4.76 Gb clean read data. From this, 243 870 contigs were assembled with Trinity and used to construct 92 792 unigenes. Distinct genes were then annotated with blastx yielding 30 810 unigenes above the cut‐off E‐value set at 10 −5 , with ESTS can database query analyses yielding up to 5366 unigenes to known hits. The identification of genes directly involved in sperm development ( DEAD ‐box family proteins), motility, fertilization and signalling (Bindin/Speract receptor) are also discussed.