Molecular phylogeny of extant horseshoe crabs (Xiphosura, Limulidae) indicates Paleogene diversification of Asian species

► Here we resolve the evolutionary history of the four living species of horseshoe crabs. ► We find that the relationship between the species matches the current taxonomy. ► We find indications for cryptic speciation across the Thai-Malay Peninsula in Carcinoscorpius rotundicauda. ► We find that the diversification of the Asian species occurred during the Paleogene.