Calanus finmarchicus, like many other copepods in the family Calanidae, can enter into a facultative diapause during the last juvenile phase (fifth copepodid, C5) to enable survival during unfavorable periods. Diapause is essential to the persistence of Calanus populations and profoundly impacts energy flow within oceanic ecosystems, yet regulation of diapause is not understood in these animals. Transcriptional profiling has begun to provide insight into metabolic changes occurring as C. finmarchicus prepares for and enters into diapause or skips diapause to prepare for the terminal molt. In particular, components of the glycolysis, pentose phosphate and lipid synthesis pathways are upregulated early in the C5 stage when lipid stores are low. Currently, our ability to identify metabolic patterns is limited by the incomplete functional annotation of the C. finmarchicus transcriptome. Such limitations are widespread among studies of non-model organisms and addressing them should be a priority for future research. In addition, integrating the results across multiple emerging complementary transcriptomic studies will provide a more complete picture of copepod physiology than isolated studies. Ultimately, identifying molecular markers of copepod physiology could enable robust identification of animals preparing to enter into diapause and ultimately lead to a greatly improved understanding of diapause regulation.