Speciation is increasingly recognized as a process that can occur without complete reproductive isolation. Understanding the genetic basis of genomic barriers and the role of gene flow between divergent evolutionary lineages remains a major challenge, particularly in cryptic species. Hybridization within the brown algae genus Ectocarpus has been documented, with patterns influenced by both species-specific factors and geographical distribution (Montecinos, 2016; Montecinos et al., 2017a; Denoeud et al, bioRxiv.). However, the lack of genome-level, population-scale studies poses a significant obstacle to understanding when introgression occurred, which genomic regions are subject to gene flow, and what mechanisms maintain genomic integrity. The cryptic species pair E. siliculosus and E. crouaniorum diverged approximately 15 million years ago (Denoeud et al, bioRxiv.). Evidence of admixture has been detected at microsatellite loci (Montecinos et al., 2017b), with introgression appearing more pronounced in the diploid stage (after syngamy) than in the haploid stage (after meiosis). Using the linked-read sequencing approach known as haplotagging (Meier et al., 2021), we reconstructed haplotypes from hundreds of diploid samples, including potential hybrids. This study investigates patterns of introgression across hybridization zones between these two cryptic species. By leveraging a population-scale genomic dataset, we aim to unravel how genome-wide introgression varies across geographic contexts and the evolutionary history of these populations.