Astragalus jaegerianus Munz (the Lane Mountain milkvetch) is a federally endangered species that exists in only four fragmented populations within and adjacent to the U.S. Army's National Training Center, Fort Irwin, CA. Since 1999, our monitored A. jaegerianus populations have consistently declined, and are now 12% of their previous size. A number of subpopulations are in danger of local extinction. The decline of A. jaegerianus has occurred simultaneously with severe drought in the Mojave Desert. These drought conditions began in 1999 and are predicted to continue for decades, or may continue indefinitely under warmer temperature conditions projected by global climate change-type drought. Our results suggest that drought has direct and indirect affects on A. jaegerianus by killing or degrading its host shrubs. Astragalus jaegerianus host shrubs have decreased in shrub volume and cover by roughly 10 percent since the onset of drought, and shrub mortality has been high. Our results show that canopy condition has a profound affect on the microclimate within host shrubs. Furthermore, our results show a significant increase in survival of A. jaegerianus among host plants with more intact canopies. These results support our study hypothesis that drought-related changes to host plant canopies affect A. jaegerianus survival, and represent an indirect negative effect of long-term drought on A. jaegerianus populations.