It is well known that first study of animal biodiversity is based on morphological, chromosomal and biochemical markers. Most of them are limited by gender, age and environment. In the last years with a significant progress in molecular biological techniques are discovered the molecular markers. They play a key role on population and species diversity. Molecular markers are specific pieces of DNA that can be identified within the genome and are inherited according to Mendel’s laws. They can be successfully utilized to detect mechanisms of polymorphic traits that contribute to genetic diversity. Moreover, molecular markers enable the detection of genetic variants at DNA sequence level are devoid of these limitations typical for morphological, chromosomal, protein markers and not influenced by environment.