The application of genetics for the management of natural resources is expanding, and within this field, DNA registers will play an increasing role. The Norwegian minke whale DNA register, established in 1996, was designed primarily as a control system to detect any attempts at illegal trade of products derived from other stocks of minke whale, or other whale species, under cover of the legal Norwegian harvest originating from the Northeast Atlantic. The register contains genetic data for 7644 of 7751 whales landed in the period 1997–2010. Profiles are established from sequencing part of the mtDNA control region, analysis of 10 STRs and a sex-determining marker. Probabilities of genotypes matching between two randomly selected whales are 6.0−04 and 3.0−08 for five and eight of the STR loci, respectively. This permits verification of traded whale products via match to the register. The register has also been used in a number of ad hoc scientific studies resulting through the accumulation of genetic, demographic and biological data. Here, we review the register’s logistics, specifications and evaluate the potential to apply similar registers to control the exploitation of other marine species.