The stone crayfish (Austropotamobius torrentium) is one of four native Croatian crayfish species that inhabits mainly cold brooks on higher altitudes. Phylogenetic relationships among different populations of this species are not yet completely resolved. In this research we have studied morphological characteristics and phylogenetic relationships of 61 individuals (37 males and 24 females) that have been collected from nine sites situated in Žumberak - Samoborsko gorje Nature Park. For molecular phylogenetic analyses we used mitochondrial genes for large ribosomal unit (16S rRNA) and for subunit I of citocrom oxidase (COI). Sequence divergences and nucleotide diversity were calculated and Bayesian analysis was applied for constructing filogenetic trees and correlating these sequences with sequences of stone crayfish from other parts of Croatia and Europe and those retrieved from on-line data-bases. Time of divergence was calculated according to the molecular clock for mitochondrial COI gene. In morphological aspect of research we measured 23 morphometrical and five meristic characteristics, which were then grouped in accordance with the results of previous genetic analyses and processed with statistical methods. Obtained results show a large genetic diversity of populations of stone crayfish in the area of Žumberak – Samoborsko gorje Nature Park. Populations can be divided into four distinctive haplogroups (Dunav, Gorski Kotar, Zeleni Vir and Žumberak/Plitvice/Bjelolasica), and the colonization of these part of Europe that followed the Pleistocenic ice ages can be retraced by consulting times of divergence and genetic diversity. Statistical analyses of morphological data shows significant differences for geographically separated populations, and discriminant analysis yielded a very high percent of correct classifications. However, since these differences were apparent only after grouping and statistically analizing the data, it is possible that this is a case of cryptic species/subspecies. Such high genetic diversity and morphological variation in populations of stone crayfish in Žumberak – Samoborsko gorje Nature Park represents an unique phenomenum on the European scale and will demand special care and protection in the near future.