Based on molecular data this is not a natural classification however, as the ciscoes are polyphyletic, comprising two different lineages within the freshwater whitefishes.

They exhibit different habitat distributions, feeding and breeding habits and morphological adaptations e.g. in their gill raker numbers.

Therefore, it has been suggested that they should not be recognized formally as distinct taxa, but all considered members of a single species, Coregonus artedi (sensu lato).

The fishery continued as cisco stocks fell and non-native species such as sea lamprey, rainbow smelt and alewife spread through the system and increased in abundance.

Within some species, geographically separated populations have been treated as distinct taxa, despite close genetic relationships, such as the vendace and the pollan (Arctic cisco) on the British Isles.