Marker Assisted Selection (MAS) for allele enrichment is widely used in plant breeding and allows for selection of difficult traits, cost effective selection in early generations and pyramiding resistance. Two fundamental traits for Australian barley production are resistance to Cereal Cyst Nematode (CCN, Heterodera avenae) and improved malt extract. Yield reduction can occur from a buildup of CCN levels in the farming system which has driven the production of CCN resistant varieties. Sloop SA was the first barley variety in the world to be produced using MAS for CCN resistance. The primary economic parameter for a successful variety in the malting and brewing industry is the level of malt extract. Thin husk has been well characterized and confers increased malt extract; both traits have been mapped to the 2HS loci in Haruna nijo x Galleon mapping population. MAS of Ha2 and Ha4 CCN resistance and 1H, 2HS, 2HL and 5H malt extract loci has progressively increased in Australian breeding programs. Consequently, crossing and MAS strategies have been devised to introgress the traits across a broad range of germplasm. The response to genotypic and phenotypic selection for increased frequency of lines with high malt extract and CCN resistance within the University of Adelaide Barley Program is examined over 14 and 16 seasons respectively (in the period 1995-2010). The results are discussed in terms of the phenotypic response, quantified impact, to MAS for malt extract and CCN loci in a breeding program.