Genetic data suggests that sockeye were native to the system before the stocking of Baker fish. There were both native sockeye and kokanee. The sockeye were in north end (Big Bear) and Sammamish. The Baker stock, based one recent genetic studies, colonized the Cedar and the lacustrine spawners in the southern lake.

Steelhead and Chinook were both native, including a Spring run that was still marginally around in the 70s. Stocking, particularly at Issaquah and the UW, brought in lots of "foreign" stocks.

I have seen some thoughts that the original mykiss in the watershed ("original" being in the 50s) was primarily resident. Stocking of Chambers Creek fish enhanced an anadromous component but they likely had little genetic impact because Chambers fish tend to be reproductively incompetent. Mykiss tend to switch from anadromous to resident and back again depending on environmental conditions. I believe that one of the drivers of the anadromous crash in the system is that being anadromous, predation on juveniles and adults from the locks to the ocean and back again and the really poor situation of moving fresh/salt and salt to fresh (immediate rather than gradual) makes being resident and better life choice.

That said, changes in flow, temperatures, development, and so on suggest to me that walleye are a more likely choice for a dominant species in the watershed.