In recent years, great progress in canine molecular genetics has been observed. DNA sequencing of a female Boxer was started in 2003. The next version of the dog genome sequence is now available online. Recently a microchip SNP array, covering over 170 thousand SNPs, has also become available. Simultaneously with the development of genetic maps and increasing accuracy of sequencing, a large number of causal mutations for various traits were identified. Most mutations were responsible for monogenic inherited diseases in dogs, but also for other traits. To date, candidate genes as markers for the size, colour and structure of hair, skeletal metric traits, behaviour and physiological traits were identified. At present, research of quantitative trait loci (QTL), analysis of candidate genes, and genome-wide association studies (GWAS) are carried out in dogs. In addition, the dog has become an animal model for many human hereditary diseases, as well as for farm animals. Recent studies primarily consist in determination of causal mutations that can lead to the development of genetic diseases, occurring in both dogs and humans. In the future, the results can be used to develop new treatments for inherited diseases in both species.