Hypoxia has profound and diverse effects on aerobic organisms, disrupting oxidative phosphorylation and activating several protective pathways. Predictions have been made that exposure to mild intermittent hypoxia may be protective against more severe exposure and may extend lifespan. Here we report the lifespan effects of chronic, mild, intermittent hypoxia and short-term survival in acute severe hypoxia in four clones of Daphnia magna originating from either permanent or intermittent habitats. We test the hypothesis that acclimation to chronic mild intermittent hypoxia can extend lifespan through activation of antioxidant and stress-tolerance pathways and increase survival in acute severe hypoxia through activation of oxygen transport and storage proteins and adjustment to carbohydrate metabolism. Unexpectedly, we show that chronic hypoxia extended the lifespan in the two clones originating from intermittent habitats but had the opposite effect in the two clones from permanent habitats, which also showed lower tolerance to acute hypoxia. Exposure to chronic hypoxia did not protect against acute hypoxia to the contrary, Daphnia from the chronic hypoxia treatment had lower acute hypoxia tolerance than normoxic controls. Few transcripts changed their abundance in response to the chronic hypoxia treatment in any of the clones. After 12 hours of acute hypoxia treatment, the transcriptional response was more pronounced, with numerous protein-coding genes with functionality in oxygen transport, mitochondrial and respiratory metabolism, and gluconeogenesis, showing up-regulation. While clones from intermittent habitats showed somewhat stronger differential expression in response to acute hypoxia than those from permanent habitats, contrary to predictions, there were no significant hypoxia-by-habitat of origin or chronic-by-acute treatment interactions. GO enrichment analysis revealed a possible hypoxia tolerance role by accelerating the molting cycle and regulating neuron survival through up-regulation of cuticular proteins and neurotrophins, respectively. Overall design: Daphnia magna from four clones (FI-FSP1-16-2, IL-M1-8, GB-EL75-69, HU-K-6, Daphnia stock collection, Basel, Switzerland) were reared either in normoxia (dissolved oxygen (DO) concentration adjusted twice daily to 8 mg/L) or in chromic mild intermittent hypoxia (DO concentration adjusted twice daily to 4 mg/L). Daphnia from both treatments were then either exposed to acute hypoxia (DO <1 mg/L) for 12 hours, or taken directly form the 8 mg/L or 4 mg/L treatments without acute hypoxia exposure. Thus the four treatments formed a 2x2 full factorial fashion with respect to chronic and acute hypoxia: Daphnia reared at normoxia Daphnia reared at normoxia and exposed to acute hypoxia for 12 hours Daphnia reared in chronic mild hypoxia and Daphnia reared in chronic mild hypoxia and exposed to acute hypoxia for 12 hours. Each sample consisted of two adult females pooled together. RNA was extracted using Qiagen RNAeasy kit (Cat ID: 74134) and quantified using a Qubit (ThermoFisher) fluorometer. Following extraction, RNAs were reverse transcribed and sequencing libraries were constructed from the cDNAs as prescribed by the Oxford Nanopore Technology (Oxford, UK) PCR-cDNA Barcoding kit protocol (SQK-PCB109), with 3 biological replicates per clone per treatment, each replicate consisting of RNA extracted from two Daphnia individuals. Barcoded samples from the 4 treatments within each clone were pooled together into 3 replicate libraries, purified separately, and pooled together immediately before adding the sequencing adapter. Libraries were then sequenced using Oxford Nanopore MinION for 24-48 hours per sequencing run, obtaining 2-4 Gb of reads in each run.