Molecular markers allow a characterization of animal populations on DNA level. They help to estimate the genetic variability, they are useful in paternity control, to diagnose hereditary diseases, in epidemiology and last but not least support traditional tools to take breeding decisions. Seventy-six new-world camelids in Switzerland were genetically typed for six microsatellite markers and their parentage controlled. Calculation of allele frequencies, heterozygosity, polymorphism information content, deviation from Hardy-Weinberg equilibrium and exclusion probability of markers showed a high genetic variability within the chosen populations. This will allow selection for certain traits. The estimated genetic distance between different camelid species and breeds was in accordance with their expected phylogenetic origins.