Abstract Geographic chromosomal variation, which in many instances does not correlate with variation in phenotype, is increasingly being detected within both large and small species of mammals. We argue that this cryptic chromosome variation can pose a significant threat to translocation practices involving the admixture of specimens between geographically distant populations. Matings between individuals characterized by different cytotypes can result in perinatal mortality or, at a later stage, in reduced fertility of offspring heterozygous for chromosomal rearrangements. This can thus impact heavily on the species, or population, that management is trying to conserve. Some of the more frequently encountered structural rearrangements in mammals and the possible deleterious effects that these can have in the heterozygous condition are reviewed and guidelines proposed for the use of cytogenetics as a conservation tool in wildlife management.