Yellow starthistle is a problematic invasive plant in the western United States. Attempts to control it often include the use of herbicides although herbicides can have detrimental effects on desired native species. We studied the effect of clopyralid on a native bunchgrass and vernal pool community in the Central Valley of California. Areas invaded by yellow starthistle were treated with clopyralid, and the presence and cover of all species was monitored for 2 yr. There were significant differences in species cover between treated and untreated plots 2 yr after treatment (P = 0.0001). These included a decline in cover of yellow starthistle and other native and exotic members of the Asteraceae and Apiaceae families in both years and a decline of exotic members of the Fabaceae family in the second year. There also were decreases in the frequency of the Asteraceae (P < 0.0001), Apiaceae (P < 0.05), Fabaceae (P < 0.05), and Polygonaceae (P < 0.05) families 1 yr after treatment, and the Asteraceae (P < 0.05) and Fabaceae (P < 0.05) families 2 yr after treatment. We also observed a significant negative effect of clopyralid on fecundity measures of a native Viola species during the first year of application (P = 0.0074). This effect did not persist into the second year, when violets were more common and produced more flowers in treated plots (0.02 < P < 0.05).