Berry crops include, but are not limited to the members of the genera: Fragaria (strawberry; Rosaceae), Rubus (brambles: raspberry and blackberry; Rosaceae), Vaccinium (blueberry, cranberry and lingonberry; Ericaceae) and Ribes (currant and gooseberry; Grossulariaceae). Berry fruits contain relatively high levels of vitamin C, cellulose, and pectin, and produce anthocyanins which have important therapeutic values, including antitumor, antiulcer, antioxidant and anti-inflammatory activities. Blueberry, cranberry and lingonberry are three Vaccinium fruit crops of economic importance which have been domesticated in the twentieth century. Cloudberry (Rubus chamaemorus L., family Rosaceae) is a less know small fruit of medicinal importance. The roseroot (Rhodiola rosea L.), also called golden root or arctic root, is used as an adaptogen in herbal medicine and is valued for its ability to enhance human resistance to stress or fatigue and promote longevity. There is a pressing need to develop reliable methods for conserving, maintaining and identifying berry germplasm and for assessing genetic biodiversity for practical breeding purposes and proprietary-rights protection. The introduction of molecular biology techniques, such as DNA-based markers, allows direct comparison of different genetic material independent of environmental influences. This paper presents the progress in-depth of various aspects of molecular diversity analyses in wild berry species and cultivars collected from Canada, Europe and USA. Inter simple sequence repeat (ISSR), random amplified polymorphic DNA (RAPD), expressed sequence tag-polymerase chain reaction (EST-PCR) and EST-simple sequence repeat (SSR) markers detected a sufficient degree of polymorphism to differentiate among wild clones and cultivars, making these technologies valuable for cultivar identification and for the more efficient choice of parents in berry breeding programs. Tremendous progress in plant tissue culture, resulting in great advances in micropropagation, has also been occurred. Although automation of micropropagation in bioreactors has been advanced as a possible way of reducing propagation cost, optimal plant production depends upon better understanding of physiological and biochemical responses of plant to the signals of culture microenvironment and an optimization of specific physical and chemical culture conditions to control the morphogenesis of berry plants in liquid culture systems. The paper describes the progress in-depth of various aspects of molecular characterization of berry and roseroot germplasm, their propagation and maintenance, and on the employment of molecular markers for the assessment of genetic fidelity, uniformity, stability and trueness-to-type among donor plants and tissue culture regenerants.