In a joint analysis of nuclear (allozyme) and mitochondrial markers (sequence and restriction fragment length polymorphism (RFLP) analysis of the 12S and 16S genes), five genetically distinct groups of the Austropotamobius pallipes Lereboullet species complex were detected in the Alpine region. The geographical distribution of these evolutionary lineages coincided largely with several taxa (A.p. pallipes, A. berndhauseri, A.(p.) italicus) formerly defined on the basis of morphological characters. A low level of genetic variability was found within these lineages. For some populations, the combination of the two markers gave additional information about the likelihood of their natural or artificial origin. A hybrid zone was detected between A.p. pallipes and A. berndhauseri in the Lake Geneva area. The mosaic distribution of the five evolutionary lineages indicated that conservation efforts should be aimed at the level of local populations.