The genus Vaccinium L. belongs to the family Ericaceae and consists of about 400 species, which are interspersed through out the world except Australia. The berries produced by the genus are edible; their flavour varies from insipid to tart to sweet. Blueberry, cranberry and lingonberry are three Vaccinium fruit crops of economic importance which have been domesticated in the twentieth century. Vaccinium fruits contain relatively high levels of vitamin C, cellulose and pectin, and produce anthocyanins which have important therapeutic values, including antitumor, antiulcer, antioxidant and antiinflammatory activities. There is a pressing need to develop reliable methods for identifying Vaccinium germplasm and for assessing genetic diversity/relatedness in Vaccinium genotypes for practical breeding purposes and proprietary-rights protection. Molecular markers are increasingly used in breeding programmes of many horticultural crops. The introduction of molecular biology techniques, such as DNA-based markers, allows direct comparison of different genetic material independent of environmental influences. In Vaccinium, genetic transformation has been developed using tissue culture systems with varying rates of success. This review presents the progress in-depth of various aspects of Vaccinium fingerprinting, DNA markers and functional genomics for the improvement of this species. It also discusses the issues that still need to be addressed to utilize the full potential of molecular techniques to develop improved cultivars suited to the changing needs of growers and consumers.