The Italian river buffalo was characterized by an extensive period of isolation, which did not allow crossbreeding. This has brought to a morpho-functional differentiation of the Mediterranean type, whose population has increased 19 fold in Italy in the past fifty years. This increase is mainly due to the rising interest in the productive characteristics of this rustic animal; actually bred mainly as dairy purpose animal. Marker assisted selection (MAS) might be a promising choice for planning appropriate breeding schemes for Italian river buffaloes. In this respect, the genetic markers significantly associated to milk yield traits may give the right information for the identification of animals with high breeding value. The literature associated with different aspects of the genetic progress in buffalo is abundant, and this chapter is a review of the molecular bases for the improvement of the quali-quantitative characteristics of the Italian dairy buffaloes occurred during the last decade.