Catastrophic events like climatic changes can lead to a drastic decline and loss of populations in widespread species. Small refugia can shield relict populations from extinction and are of great importance for maintaining genetic diversity and for recolonization events. In the giant centipede Scolopendra cingulata Latreille, 1829, widely distributed along the Mediterranean Sea, the northern-most populations occur in isolated microrefugia in Austria and Hungary. The origin and relationships of these populations remain largely unknown. Here we describe a second, previously unknown, microrefugial population of S. cingulata from Austria and provide insights into the evolutionary history of the northern-most populations of the species based on molecular analyses (COI) of 16 populations. Our results show that the Austrian and Croatian populations are closely related, while genetically distinct from the Hungarian and Romanian representatives. Therefore, we conclude that the northern-most populations of S. cingulata are relicts from multiple independent post-glacial recolonization events from southern refugia.