Knowing the metapopulation structure of the American lobster is a key point for the management and the sustainability of fisheries. Indeed, if we could identify the different populations and their connectivity, we would be more able to understand the stocks variability, both at the national and the local scales. Here, the main goal of our study is to answer the question: What is the metapopulation structure in the American lobster? A previous study has revealed a weak genetic structure in the American lobster by using 13 molecular markers (Kenchington et al. 2009). Due to the small number of molecular markers used to obtain those results, it should be pertinent to reassess the genetic structure of this species. Here, we will use more than 5000 markers in order to highlight the genetic structure of the American lobster with a higher resolution. In addition, there is currently no information on the effect of selection in the American lobster. However this species occupies different habitats, which could lead to divergent selection and local adaptation. In order to more rigorously assess genetic structure of this species and to test the local adaptation hypothesis, we are going to develop new molecular markers called SNPs (single nucleotide polymorphisms). For that purpose, we will use a new technique called Genotyping by Sequencing (GBS) with the aim of identifying thousands of markers. Between 30 to 50 individuals will be sampled per site at a total of 20 sites. The sampling plan was based on the delimited Lobster Fisheries Areas (LFA) in order to reveal the genetic structure within and among LFAs. This plan was defined in conjunction with the different partners of the project: fishermen, government scientists, and the academic scientists. The genetic structure observed will be linked to several environmental factors such as the currents circulation, which has an important impact on the genetic structure and the connectivity, as well as the variation of the temperature (surface and bottom) and the salinity, which could affect the connectivity and favour the local adaptation.