Atlantic cod (Gadus morhua) in the Skagerrak consists of two genetically distinct ecotypes, coastal cod and offshore cod, which remain largely reproductively isolated despite spawning in overlapping coastal areas. Although both ecotypes have been documented spawning within the same fjords, hybrids are remarkably rare in the wild, suggesting the presence of strong reproductive barriers. The Swedish–Norwegian research project CODTYPES aims to identify the ecological and evolutionary mechanisms maintaining this divergence by investigating how behavioural processes, genomic architecture, and natural selection interact to limit hybridization. To address these questions, we established a unique multi-generational experimental system in which 45 wild-caught adult cod were allowed to spawn naturally in a large semi-natural seawater pond at the Flødevigen Research Station (Norway). Eggs, larvae, and juveniles were sampled throughout the spawning season, and the offspring were reared to sexual maturity before reproducing naturally during the 2024–2025 spawning season. By combining genomic data from the wild-caught parental generation (F0) and two successive offspring generations (F1 and F2), we can quantify the contributions of mate choice, genomic architecture, and natural selection to hybridization across three generations. Whole-genome sequencing (Illumina NovaSeq X Plus; approximately 20x coverage) will generate high-resolution genomic data from 300 individuals, enabling parentage reconstruction, pedigree inference, and genome-wide analyses of inheritance patterns within and across ecotypes. These analyses will reveal the extent of assortative mating, fitness, and reproductive success among pure-ecotype and hybrid individuals. We will then compare observed inheritance patterns with neutral expectations to identify genomic regions under selection. A central focus of the project is to determine how structural genomic variation, particularly the four large chromosomal inversions ("supergenes") known in Atlantic cod, influences introgression between ecotypes. These inversions are thought to facilitate local adaptation by reducing recombination, yet their role in maintaining reproductive isolation remains unknown. By comparing inheritance and introgression patterns within and outside inversion regions, we will directly test whether structural variants act as genomic barriers to gene flow. This study represents the first opportunity to investigate genome-wide selection across three generations in Atlantic cod, providing an unprecedented experimental framework for understanding the mechanisms that maintain divergence despite ongoing opportunities for hybridization. We expect to identify genomic regions exhibiting restricted introgression and strong selection, including candidate genes involved in oxygen transport, osmoregulation, and egg buoyancy. Beyond advancing fundamental evolutionary biology, the results will improve our understanding of adaptive variation in Atlantic cod and provide essential knowledge for the sustainable management and conservation of coastal cod populations in the Skagerrak under future environmental change.