The primary goal of this study was to reveal the most transcribed gene functions of the prokaryotes associated with S. carteri. Stylissa carteri specimens (n=3) were collected at Fsar reef (22°23’N 39°03’E) at the coast of Thuwal, Saudi Arabia. The collection occurred with water temperature at 30 °C, at 13-14 meters depth, on 2nd November 2010. Enriched prokaryotic mRNA was obtained from total RNA extracted from RNAlater-preserved sponge tissues. Enriched prokaryotic mRNA was amplified and pair-ended sequenced using Illumina HiSeq 2000 standard protocols.