The Win95 program for computation of distance matrixes and construction of phylogenetic or phenetic trees on the basis of RAPD, RFLP and allozyme data was presented. In contrast with other presently available software, the program FreeTree can also assess the robustness of the tree topology by bootstrap, jackknife or OTU-jackknife analysis. Moreover, the program can be used also for an analysis of data obtained in several independent experiments performed with nonidentical subsets of taxa. The function of the program was demonstrated by an analysis of RAPD data from 22 strains of Frenkelia. The program is available as an autoextractive archive containing the installation files of FreeTree and TreeView, manual in MS Word format and a sample of the input file at http://www.natur.cuni.cz/flegr/programs/+ ++freetree.