After California black rails were discovered at the UC Sierra Foothill Research and Extension Center in 1994, an extensive population of this rare, secretive marsh bird was found inhabiting palustrine emergent persistent (PEM1) wetlands throughout the northern Sierra Nevada foothills. We inventoried a variety of PEM1 wetlands to determine which habitats would likely support black rails. Black rails were positively associated with larger PEM1 wetlands that had flowing water, dense vegetation and irrigation water as a primary source; they were negatively associated with fringe wetlands and seasonal water regimes. Recommendations for managing black rail habitat in the northern Sierra foothills include prioritizing the conservation of PEM1 wetlands with permanently or semipermanently flooded water regimes and shallow water zones (less than 1.2 inches), especially those that are greater than 0.25 acres in size; avoiding wetland vegetation removal or overgrazing, especially during the black rail breeding season (approximately March through July); maintaining and improving wetland connectivity; ensuring that impacts to black rails are considered in the environmental review process for development projects; and integrating management guidelines for black rails into existing wetland conservation programs.