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EXECUTIVE SUMMARY Sampling was undertaken in a reach of the Yampa River (RK 161-199.6), near Maybell, Colorado, from 2003-2006 to determine native fish response in control and treatment reaches to removal ofnon-native predator fishes in treatment reach. Removal in the treatment reach focused on larger, age-1 or older smallmouth bass and northern pike in all years and was conducted under a separate study. In 2005 and 2006, increased effort was allocated to remove small-bodied age-0 smallmouth bass from the treatment reach. Sampling to understand native fish response to removal was conducted in both a 19.3 RK control reach and a 19.3 RK treatment reach and focused mostly on age-0, small-bodied native fishes, because response of that life stage would likely be easiest to detect. Yampa River habitat has changed since drought began in 2000, with lower stream flows and higher water temperatures. These factors were likely associated with a fish community shift since 1999 to increased abundance of smallmouth bass, and decreased diversity and abundance of native fishes in 2003-2006, in spite of predator fish removals. Sampling of 249 individual habitat areas, distributed among an array of habitat types in control and treatment reaches, showed that native mottled sculpin are no longer found in the study area despite presence of adequate riffle habitat. Al] other native fishes are now rare in mainstem Yampa River habitat and smallmouth bass is the dominant species captured in most years in both control and treatment reaches. No difference in presence or abundance of native fishes was detected in control and treatment reaches. Native fishes were captured in isolated pool habitat, in both control and treatment reaches, in significantly higher frequencies and abundances. In isolated pools, abundance of native fishes was negatively associated with presence and abundance of smallmouth bass. We also examined utility of smallmouth bass otolith analysis to better understand timing of spawning and growth rates of this species. Preliminary studies showed promise and additional information gathered under different flow iii