There is some debate as to whether the kokanee and its sea-going relative are separate species; geographic isolation, failure to interbreed, and genetic distinction point toward a recent divergence in the history of the two groups.

The divergence most likely occurred around 15,000 years ago when a large ice melt created a series of freshwater lakes and rivers across the northern part of North America.

While some members of the salmon and trout family (salmonids) went out to sea (anadromous), others stayed behind in fresh water (non-anadromous).

While they occupy the same areas and habitats during the breeding season, when ocean-going sockeye salmon return to freshwater to spawn, the two populations do not mate with each other in some regions, suggesting speciation.

[9] There is debate as to whether the kokanee has enough genetic distinction to be classified as a subspecies or a separate species from the sockeye salmon.

The data also suggests that the kokanee may have evolved back into a lake-type anadromous form at some point in recent history, although there is a lack of interbreeding between it and sockeye in the drainage systems.

[11] Studies done in Okanagan Lake in British Columbia and Lake Sammamish in Washington State suggested that the genetic diversity between the lake-type sockeye and the kokanee marks the divergence of two species because cohabitating sockeye and kokanee did not interbreed, despite the fact that interbreeding was possible.

[13] Other morphological differences include higher gill raker counts in the kokanee, failure to develop the changes that allow the sockeye to transition between fresh and salt water, and juvenile kokanee's lower mean swim velocity compared to juvenile sockeye.

[15] Studies have found that kokanees can extract carotenoids (which provide red pigmentation during breeding) from food better than sockeyes due to sexual selection and mate choice.

In bodies of water with more favorable conditions it can reach a size of up to 51 centimetres (20 in) and weigh 1.4–2.3 kilograms (3–5 lb).

The largest documented kokanee, caught by hand in Lower Arrow Lake in British Columbia in 2015, weighed 5.5 kilograms (12.1 lb).

[19][9] As a fish that inhabits freshwater throughout their lifecycle they are often smaller than their sea-going sockeye relatives, due to less food availability.

In addition, when compared to other trout, they have finer scales, larger eyes, and deeply forked tail".

[22] Other factors such as pollution, habitat loss, and warming global temperatures put the kokanee at risk in some areas.

[23] The current IUCN red list standing of sockeye salmon (Oncohynchus nerka), which does not distinguish kokanee, is of least concern.