The work is aimed to study of morphological variability of Phytophthora alni complex in the area of the Czech Republic with use of numerical phenetics. The morphological analysis of 29 Phytophthora alni strains acquired from the area of the pathogen in the Czech Republic was carried out. In total there were studied 50 cultural and morphological characteristics: 14 cultural characteristics, 16 characteristics describing asexual and 20 characteristics describing sexual structures. The all morphological measurements were repeated twenty times at magnification 1600× with use of Olympus BH-2 microscope, Olympus E-510 camera and Quick Photocamera 2.3 measuring software. The data were processed in Statistica 8.0 in modules of non-parametric statistics, descriptive statistics, cluster analysis, analysis of principal components and discriminant analysis. In the area there was confirmed the presence of the two taxa belonging to the P. alni complex: Phytophthora alni subsp. alni (Paa) a Phytophthora alni subsp. uniformis (Pau). The third taxon (P. alni subsp. multiformis) was not found. The nominate subspecies Paa prevailed - more than 4/5 of studied isolates belonged to this taxon. The classification of isolates was in full agreement with molecular study of identical set of isolates which was parallely performed (Štěpánková et al. 2013). The morphological analysis showed, that majority of Czech isolates of P. alni complex can be successfully determined on the basis of standard morphological characters -- oogonial wall ornamentation, antheridial length, rate of aborted oogonia etc. Ca 10 % of isolates were found to be intermediate. All studied isolates were divided with series of cluster and PCA analysis in two relevant clusters and a discriminant function dividing the isolates in the two taxa on basis of morphological characters was generated and validated. The rate of standard oogonia, high of oogonial ornamentation, rate of two-celled antheridia with central septum and antheridial length were used as discriminators. The two different Paa morphotypes were found in the area of the Czech Republic. The discriminant function dividing the Paa isolates in these two morphotypes was also constructed and tested. The discriminators were oogonia diameter, high of oogonial ornamentation and width of antheridium. The most reliable character was the antheridial width: the north-western morphotype has antheridia wider by 3 micrometres than the south-eastern one. The Paa taxon was continuously distributed in the western part of the area, its frequency diminshes eastward. The distribution of the second taxon - Pau - was scattered and insular, but it was found out in the whole area of the Czech Republic. It could be supposed, that the parental taxon Pau had spread before Paa invasion in the area. Later the new and more combative Paa replaced the older weakly pathogenic Pau. The recent area of Pau is apparently insular and probably relict. The two Paa morphotypes importantly differ in their distribution - the first morphotype is more frequent in north-western part of the area (and predominates in western, central and northern Bohemia) while the second one is frequent in the south-eastern part (southern Bohemia and Moravia). Likely, these two subpopulations can represent the remains of colonisation waves of two allopatric Paa lineages. The lineages can originated by repeated independent hybridisation between parental Pau and Pam taxa somewhere in western or central Europe.