The Harpacticoid copepod Tigriopus brevicornis belongs to the meiofauna of intertidal rock pools and is distributed widely along European coasts. Sixteen sites were sampled from the Irish Sea to the coasts of Spain. We used the ITS1 marker to analyse the relationship between the populations because it shows low intrapopulational variation (mean pairwise difference: 1.00 ± 0.8) and high interpopulational divergence (mean pairwise difference: 16.38 ± 7.39). A total of 57 bp out of 433 bp were recognised as informative nucleotides among the 61 individuals analysed. The analysis of the genetic relationships highlighted a north-south split in the distribution of the natural populations and showed a genetic break point around the Gironde estuary, which is probably due to differences in the geomorphologic characteristics of the coastal area on the two different sides of this estuary. Various populations were isolated and the ITS1 sequences indicated that there are specific genetic signatures in these populations. The northern set of populations, which was sampled along a large rocky coastline, had a metapopulation structure with genetic exchanges between geographically close populations and also between geographically far ones. The southern set of populations, which was sampled in small rocky pools on large sandy beaches, showed isolated populations as a consequence of the geomorphology of the area