Allele-specific expression (ASE) is now a molecular mechanism widely studied at the cell and organism-levels. However, population-level ASE and its evolutive impacts have still never been investigated. Here, we deciphered the potential link between ASE and natural selection. As a model, we used metagenomic and metatranscriptomic data of seven wild populations of the marine copepod Oithona similis from Tara Consortium sampling in the Arctic Seas. We were able to (i) Study the structure between these populations, (ii) Detect variants under local adaptation, iii) Develop a method to detect variants under ASE. We found a significant amount of variants under ASE in at least one population and under selection across all the populations, proving that a link exists between these two molecular mechanisms. The next step of this work is to determine the nature of the link between ASE and selection.