The goal of this project is to survey and inventory species identified in the Comprehensive Fish and Wildlife Conservation Plan as being in need of inventory. In the Yellowstone River drainage, small and non-game fishes were sampled in the mainstream Yellowstone River from the mouth of the Clarks Fork downstream to the confluence with the Missouri River in North Dakota. Sampling efforts have resulted in thousands of fish captures, providing researchers with insights into species-habitat associations, the importance of connected habitats, and shifts in seasonal use of habitats. Structured western pearlshell mussel surveys were completed in 18 watersheds on 266 stream reach visits in Western Montana. Early results from Western Pearlshell surveys indicate that 25 of the 40 originally reported pearlshell sites were extirpated or not viable. Further results on otolith microchemistry analysis and a statewide mussel survey can be found in the associated reference reports.