The cnidarian Hydra exhibits extremely low senescence when maintained in homeostatic conditions. However H. oligactis animals that undergo sexual differentiation upon transfer from 18°C to 10°C, exhibit a visible aging. Our laboratory characterized two H. oligactis male strains that exhibit different phenotypes once they enter gametogenesis: the cold-sensitive strain (Ho_CS) that exhibits a typical cold-induced degenerative phenotype, and the cold-resistant strain (Ho_CR) that returns to homeostasis. In this study, we performed a large-scale comparative transcriptomic analysis to identify structural as well as regulatory genetic differences between these two strains. We identified a TNF receptor-associated factor (TRAF) that shows a series of deletions in Ho_CS when compared to Ho_CR. We also characterized genes differentially expressed over time between the two strains, such as CIRBP, IMPDH1, TRPA1 and TRPM3, which are orthologs to human proteins involved in response to cold or sensory perception of temperature stimulus, as well as sequences that encode uncharacterized proteins. Moreover, we characterized genes reported in the Human Ageing Genomic Resources (HAGR) GenAge database revealed supplementary interesting candidates such as orthologs for AIFM1, EIF5A2, ERCC4, GCLC, GSK3A, HDAC, HSPD1, MLH1, MAPK3, SOCS2, TRAP1, UCHL1 and ZMPSTE24, which are temporarily differentially expressed between the two strains. TRAP1 and HSPD1 are heat shock proteins, the latter being also involved in the response to cold. We thus retrieved interesting genes candidates that may influence aging phenotype following exposure to cold in Hydra.