The utility of 15 new and 17 previously published microsatellite markers was evaluated for
species identification and stock delimitation in the deep-water hake Merluccius paradoxus and
the shallow-water hake Merluccius capensis. A total of 14 microsatellites was polymorphic in M.
paradoxus and 10 in M. capensis. Two markers could individually discriminate the species using
Bayesian clustering methods and a statistical power analysis showed that the set of markers for
each species is likely to detect subtle genetic differentiation (FST < 0.006), which will be valuable
to delimit and characterise genetic stocks.