CSIRO has established an effective breeding program that continues to deliver high yielding and high performing varieties containing transgenic traits for more sustainable and profitable insect and weed control. To stay competitive globally, new varieties must be developed more rapidly and efficiently and this can only be achieved through the adoption of biotechnology and modern molecular marker techniques. Over the last 15 years the Canberra Biotech team has augmented the efforts of CSIRO's breeders to allow the introduction of Monsanto's Ingard, Roundup Ready, and later Bollgard II and Roundup Ready Flex traits into elite germplasm that has had a significant impact on the economics and environmental footprint of cotton. As the conventional variety suite is expanded each new variety must be converted by repeated backcrossing to BG II/RRF (or any new transgenic trait introduced into the program) and this requires extensive molecular screening to follow the traits (all three genes segregate independently) through segregating populations. This is carried out in Canberra by high throughput biochemical and DNA screening methods that detect the Bt protein or site of insertion of the transgene, effectively molecular markers for each of the traits. Molecular markers for disease, yield or quality determinants could be used in a similar way in our conventional breeding to reduce population sizes before extensive field testing is needed and would accelerate CSIRO's output if the right markers could be found. Some markers reportedly linked to good fibre quality have been published, but we need to establish that they are relevant to our germplasm. Yield is also critical to cotton and if we had a better understanding of the genetic determinants of yield we might more effectively select for varieties with both high yield and quality or manipulate yield by GM to keep Australian cotton ahead of its competitors.