The stable fly, Stomoxys calcitrans L. (Diptera: Muscidae), is one of the most significant pests of livestock in the United States. The identification of targets for the development of novel control for this pest species, focusing on those molecules that play a role in successful feeding and reproduction, is critical to mitigating its impact on confined and rangeland livestock. This data set was obtained from pyrosequencing of stable fly immature and adult specimens, comprising genes expressed at these stages. Stable fly specimens were obtained from an in vitro colony that is maintained at the Knipling-Bushland U.S. Livestock Insects Research Laboratory (Kerrville, TX) at 27°C, 60% RH, and a photoperiod of 12:12 [L:D] h. The stages included 1 g each of newly laid (t0) and 24 h post-oviposition (t24) embryos, 5 g of pooled 2nd–3rd instar larvae (late larvae), 2.5 g newly pupariated pupae (early pupae), 5 g pharate adults (pupae 2 d prior to eclosion; late pupae), and 1.5 g each of heads from unfed adult females and males (adult). Total RNA was isolated from various stages using the ToTALLY RNA Isolation Kit (Ambion, Foster City, CA) following the manufacturer’s protocol. Five micrograms of normalized cDNA was prepared for sequencing on the 454/ Roche GS-FLX. Double-stranded cDNA was nebulized to generate nominal 500-kb fragments and a shotgun library prepared for GS-FLX sequencing as per the manufacturer’s instructions (Roche, Indianapolis, IN). The sequencing library was run on a full picotitre plate and resulting data submitted to NCBI Short Read Archive (SRX018014). The resulting sequence data was assembled using newbler (RocheN) and the assembly optimized using a beta version of NGEN (DNAstar, Madison, WI) and Seqman (DNAstar, Oxford, UK). BLASTx was utilized based upon W.ND-BLAST (Dowd et al., 2005) against an embl-derived database for Drosophila (2008). Functional annotations were derived using DAVID (Dennis et al., 2003). Raw reads were submitted to the Sequence Read Archive (SRA) Database at NCBI.