Productive and reproductive performance is the key driver of the efficiency and profitability of milk production system. During the last few decades, most countries have placed varying levels of emphasis on these functional traits, hence phenotypic performance has started to improve. Recently, the underlying physiological mechanisms responsible for good or poor phenotypic productivity and fertility have started to be unraveled. The poor genetic merit for production and reproduction traits is associated with multiple artifacts in a range of tissues that are antagonistic to achieving satisfactory productive performance. The genetic value of a trait indicates the likelihood that the genes responsible for that trait will be transferred to any offspring. As other livestock traits, milk production and reproduction are influenced by many genetic loci that act directly, interact with each other, and/or interact with the environment. In recent years, molecular genetics has lead to the discovery of candidate genes with substantial effects on the traits of economic importance. Molecular genetics allows understanding the genetic structure of individuals at the genomic level and may provide the tools to make those opportunities a reality. Identification of candidate gene and use it in marker-assisted selection (MAS) serves to favorably relate alleles for quantitative characteristics with information about the individual mode of action and their interaction of genes, helping to understand the quantitative variations and their practical use in animal husbandry. In conclusion, advances in molecular technology have enabled the identification of genomic regions underlying complex phenotypic traits, and incorporation of detected quantitative trait loci into genetic evaluation provides great potential to enhance selection accuracies, hence the performance of dairy animals.