In the present work, we undertook an important effort to significantly increase the number of R. philippinarum ESTs in the public databases. Specially, the aim of this work was to discover new immune-related genes using pyrosequencing on the 454 GS FLX (Roche-454 Life Sciences) platform with the Titanium reagents. To achieve this goal, we sequenced the transcriptome of R. philippinarum hemocytes previously stimulated with different pathogen-associated molecular patterns (PAMPs) to obtain the greatest number of immune-related transcripts as possible. The raw data are accessible in the NCBI Short Read Archive (Accession number: SRA046855.1).