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The corpus allatum (CA) is an endocrine organ of insects that synthesizes juvenile hormone (JH). Yet little is known regarding the global gene expression profile for the CA, although JH signaling pathway has been well-studied in insects. Here, we report the availability of the transcriptome resource of the isolated CA from the final (fifth) instar larvae of the silkworm, Bombyx mori when the JH titer is low. We also compare it with prothoracic gland (PG) that produces the precursor of 20-hydroxyecdysone (20E), to find some common features in the JH and 20E related genes between the two organs. A total of 17,262 genes were generated using a combination of genome-guided assembly and annotation, in which 10,878 unigenes were enriched in 58 Gene Ontology terms, representing almost all expressed genes in the CA of the 5th instar larvae of B. mori. Transcriptome analysis confirmed that gene for Torso, the receptor of prothoracicotropic hormone (PTTH), is present in the PG but not in the CA. Transcriptome comparison and quantitative real time-PCR indicated that 11 genes related to JH biosynthesis and regulation and six genes for 20E are expressed in both the CA and PG, suggesting that the two organs may cross talk with each other through these genes. The temporal expression profiles of the two genes for the multifunctional neurohormonal factor sericotropin precursor and the uncharacterized protein LOC114249572, the most abundant in the CA and PG transcriptomes respectively, suggested that they might play important roles in the JH and 20E biosynthesis. The present work provides new insights into the CA and PG.