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The blackberry industry needs a reliable method to ensure trueness-to-type of blackberry products. Microsatellite markers or simple sequence repeats (SSRs) are ideal for cultivar fingerprinting, paternity testing and identity certification. Fingerprinting is valuable for variety identification, quality control and as a legal method to protect against infringement by competitors. The objectives of this study were to develop a DNA extraction protocol and SSR-based identification for individually quick-frozen (IQF) ‘Marion’ and ‘Kotata’ whole berries and concentrate and to generate genetic fingerprints for 16 important western blackberry cultivars. IQF berries and frozen concentrate of ‘Marion’ and ‘Kotata’ were generously provided by reliable commercial sources. The FAST ID Kit worked better than two other DNA extraction methods for isolating DNA from IQF berries and from frozen and thawed concentrate. Out of twenty-nine SSRs tested, ten polymorphic SSRs differentiated between ‘Marion’ and ‘Kotata’ leaves and were chosen for subsequent analyses. SSR-based fingerprinting of individual IQF berries (using the receptacle for DNA extraction) revealed a mixture of ‘Kotata’ and ‘Marion’ berries in the commercial ‘Marion’ bag while fingerprinting of frozen ‘Marion’ concentrate identified ‘Kotata’ in the small frozen puree sample evaluated and possible contamination from seed DNA. The ten SSRs differentiated between each of the 16 western cultivars included in this study. In fact, one SSR marker, Rubus 275a was sufficient to distinguish these 16 cultivars. In summary, blackberry can be reliably identified with SSR markers, using leaves and frozen berries as sources of DNA. Fingerprinting from concentrate does not appear reliable for identity certification due to possible contamination from seed DNA.