This is the first transcriptome of the pathogenic protozoa B. ostreae responsible of important decline of the European endemic flat oyster population since the 50s . Because this protozoa is not yet cultivable, it remain extremely challenging to obtain high quality -omic data, and to date, except for small rRNA fragment no genomic nor transcriptomic data are available for this important zoonic pathogen. We present here the first de novo transcriptome assembly and analysis of the Flat Oyster pathogenic protozoa Bonamia ostreae.