Within the aquaculture industry downgrading losses due to poor quality represent large costs to the producers, and an interest in implementing quality parameters in breeding goals has therefore emerged. Through genome-wide association studies (GWAS) one can identify genetic variation affecting quality parameters, which can in turn facilitate efficient implementation in breeding schemes by use of marker-assisted selection. This study aimed to identify genetic variation affecting fillet fat content and fillet firmness in farmed Norwegian Atlantic salmon using 5650 genome-wide distributed SNPs. Phenotypic records from instrumental analyses of fillet fat content and fillet firmness were retrieved from fish provided by a commercial Norwegian breeding company and implemented in GWAS. Further, genome partitioning by estimation of variance components for individual chromosomes based on SNPs was conducted for the purpose of validating results from GWAS. Combined the results from GWAS and genome partitioning suggested that genetic variation affecting fillet fat content is present on Atlantic salmon chromosomes 9 and 10, and that genetic variation affecting fillet firmness is present on Atlantic salmon chromosomes 3 and 11.