Purpose: The goal of this study was to identify CNVs within SNPs data and examine adaptive population structure of American lobster populations using both SNPs and CNVs. Methods: DNA was extracted from samples collected on 1,141 wild female lobsters using muscle tissues from half of the second walking leg. Sequencing was done using a sequence capture approach so-called Rapture. The sequence capture step allows targetting a panel of informative and high quality RAD loci, which have been discovered and selected from an initial RADseq experiment. As such, these captured loci still represent a sampling of the genome-wide variation. Rapture thus represents a cost effective and flexible approach which allowed sequencing a large number of samples with a high sequencing depth, thereby enabling efficient generation of a large population genomic dataset. More specifically, we used the same 9,818 targeted loci previously used for the American lobster and all the details about the wet protocol are described in Dorant et al. (2019). All Rapture libraries were sequenced on the Ion Torrent p1v3 chip at the Plateforme d analyses genomiques of the Institute of Integrative and Systems Biology (IBIS, Universite Laval, Quebec, Canada). Two rounds of sequencing (i.e. two separated chips) were conducted for all Rapture libraries. Results: A total of 1,141 lobsters have been sequenced, yielding an average of 431 350 raw reads per sample.