Here we explore the high-altitude adaptions and acclimatisation of Aporrectodea caliginosa. Population diversity is assessed through mitochondrial barcoding, identifying closely related populations across the island of Pico (Azores). We present the first Megabase N50 assembly size (1.2 Mbp) genome for A. caliginosa is presented. High and low -altitude populations were exposed experimentally to a range of Oxygen and temperature conditions, simulating altitudinal conditions and the transcriptomic responses explored. SNP densities are assessed to identify signatures of selective pressure and their link to differentially expressed genes. The high-altitude A. caliginosa population had lower differential expression and fewer co-expressed genes between conditions indicating a more condition refined epigenetic response. Genes identified as under adaptive pressure through Fst and nucleotide diversity in the high-altitude population clustered around the differentially expressed upstream environmental response control gene, HMGB1. The high-altitude population of A. caliginosa indicated adaption and acclimatisation to high altitude conditions and suggested resilience to extreme weather events. This mechanistic understanding could help offer a strategy in further identifying other species capable of maintaining soil fertility in extreme environments.