This study elucidates to generate a linkage map for Portuguese oysters, Crassostrea angulata, and recognise potential markers linked to economical traits in C. angulata. Genome-wide association studies (GWAS) using 19,475 single nucleotide polymorphisms (SNPs) generated by a genotyping-by-sequencing approach consisting of 647 individuals in two selection generations of C. angulata, consisting of 57 full-sib family of the first generation and 33 full-sib family of the second generation. GWAS identified six significant SNPs linked to whole weight (P < 10−4). These six SNPs explained 10.2% of the total genetic variance of whole weight. Additionally, three SNPs were identified linked to meat yield (i.e., soft tissue weight) and contributed to 9.2% of the total genetic variance for this trait. By linkage analysis on the raw data, a total of 19,475 SNP markers were mapped to 10 linkage groups, with an average density of 19.1 SNPs per cM. This linkage map was developed and potential markers identified for whole weight and soft tissue weight provide a novel resource to characterise the genetic structure of economic traits in C. angulata.