Coral reefs are diverse highly productive ecosystems, hotspots for biodiversity, and have been assigned a high monetary value, however, they are threatened and understudied regarding population genetics. Cold water coral Lophelia pertusa is classified as critically endanger in Sweden and has earlier been investigated in the Skagerrak area using microsatellites, yielding coarse estimates of genetic diversity In 2013, recolonialisation of an old L. pertusa reef close toVäderöarna was discovered, however, the genetic structure and the source of origin remains unknown. The aim of this study is to investigate clonality and genetic diversity for the Tisler reef and Väderö reef in Skagerrak, as well as to explore the ancestry of the Väderö reef from the Tisler reef using whole genome resequencing.