Atlantic cod (Gadus morhua, Linnaeus 1758) in the Gulf of Maine are managed as a single stock despite several lines of evidence supporting two spawning groups (spring and winter) that overlap spatially, while exhibiting seasonal spawning isolation. Low coverage whole genome sequencing was used to evaluate the genomic population structure of Atlantic cod spawning groups in the western Gulf of Maine and Georges Bank using 222 individuals collected over multiple years. Results indicated low, temporally stable, total genomic differentiation, while also showing strong differentiation between spring and winter spawning groups at specific regions of the genome. Guided regularized random forest and ranked FST methods were used to select panels of single nucleotide polymorphisms (SNPs) that could reliably distinguish spring and winter-spawning Atlantic cod (88.5% assignment rate), as well as males and females (95.0% assignment rate) collected in the Gulf of Maine. These SNP panels represent a valuable tool for fisheries research and management of Atlantic cod in the Gulf of Maine that will aid investigations of stock production and support accuracy of future assessments.