A comparison between LSU and mtDNA sequences with respect to species level resolution for the genus Cottus. Twelve species of the genus Cottus were sequenced for both markers and trees were obtained via the neighbour joining algorithm in MEGA 3.1. For three species, multiple animals from given populations were sequenced. Both markers detect the same groupings, with the exception of the animals from the population "RotesW", where COI sequences generate a different assignment. Further analysis of this case has shown that this is due to mitochondrial transfer.