Pacific oyster has been translocated globally from its original range in coastal Asia. Naturalized populations now exist throughout the Northern Hemisphere, including in France and Western Canada. The extent of population differentiation in Western Canada and throughout its translocation range is thought to be very low. The differences between the naturalized and farmed oysters from hatcheries are not fully understood. The present work analyzes such differences using genome-wide double-digest RAD-sequencing of hundreds of individuals from naturalized or wild populations, farmed populations, and naturalized oysters moved onto farms.