Knowledge about the dispersal patterns of marine organisms is vital for understanding population dynamics and designing appropriately scaled protected areas and fisheries management. Assessing the extent to which populations are connected by larval exchange has been traditionally approached by delineating genetically differentiated populations. Inferring these patterns for species with high gene flow remains a challenge, as they often show panmixia over large spatial scales. In these cases, genetic connectivity may be revealed through the combination of population- and kinship-based approaches. Here, we assess the population structure and relatedness of the shanny Lipophrys pholis over 500 km along the Western Iberian Peninsula coastline, using 27 microsatellites developed for this study. As expected, given its long larval duration stage, we found high gene flow throughout the study area. However, a weak pattern of isolation-by-distance was detected by Mantel tests and large-scale relatedness patterns, suggesting decreasing genetic similarity with distance at the scale of the Western Iberian Peninsula. Conversely, we provided evidence of fine-scale connectivity at the smaller scale of the Atlantic Islands of Galicia National Park (Spain). Combining population- and kinship-based approaches may reveal previously undetected genetic differentiation within a well-connected population; however, we stress the importance of careful application and interpretation of relatedness metrics. Our findings may be broadened to other coastal organisms featuring similar life-history traits, including a relatively long larval phase, as well as comparable environmental conditions favoring dispersal by ocean currents, which could be directly applied to the management and conservation of Northeast Atlantic marine species.