A four-step approach using pedigree data to create genetically diverse groups of animals for genotyping from a limited pool of available samples was developed and applied to a data set comprising five endangered Austrian goat breeds. Animals were selected according to their raw gene contribution, number of offspring, average relatedness to the living population and relatedness to other selected animals. Not all criteria could be applied to the same degree to all breeds due to small number of available samples. Methods to cope with this circumstance are presented in the paper. Inbreeding coefficient was lower in the selection groups than in the total populations in all breeds. Genotype data derived from the selected animals will be used to analyse diversity parameters and compare with available data from other Alpine goat breeds.