The threespine stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to diverse freshwater habitats since the last glaciation. To study gene expression across different populations, we sequenced transcriptomes from wild-caught sticklebacks from a marine environment to compare with data from freshwater populations published with the project accessions PRJEB8677 and PRJEB26492. Genomic data from these individuals can be found under the project accession ERP001339.