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Genotyping by sequencing along with high throughput sequencing approaches allows for the rapid development and discovery of variable markers such as microsatellites, which can be highly informative for population genetics. These approaches, along with combinatorial barcoding techniques and a novel genotyping protocol, were employed to examine the population structure of commercially valuable fisheries species, Nephrops norvegicus. Results suggest at least four genetically distinct groupings of the species across the sampled distribution and the presence of isolation by distance. No evidence for genetic bottlenecks were found in any population, however the genetic structure observed in this study does not correspond to current fisheries management delineations. This study is the first to apply microsatellite markers distribution-wide for this species, revealing a population structure for Nephrops norvegicus important for informing management of this widely fished species.