Chloropyron palmatum (Ferris) Tank & J.M Egger (formerly Cordylanthus palmatus [Ferris] J. F. Macbr.) is an annual plant that inhabits seasonally flooded wetlands with saline and alkaline soils in California. In 1986, the plant was listed as endangered under the U.S. Endangered Species Act. We aimed to inform conservation strategies for the species’ five remaining populations by examining the genetic diversity and structure of the populations (on the basis of nuclear DNA markers) and their potential response to demographic and environmental stochasticity. We also assessed fluctuations in population size and whether there was evidence of hybridization between C. palmatum and Chloropyron molle (A. Gray) A. Heller subsp. hispidum (Pennell) Tank & J.M. Egger (formerly Cordylanthus mollis A. Gray subsp. hispidus [Pennell] T.I. Chuang & Heckard). Populations of C. palmatum were genetically distinct with a F_ST of 0.23, indicating substantial genetic structure among populations. Within populations, there was no evidence of isolation by distance. However, individuals in two adjacent vernal pools were genetically distinct. The pattern of genetic variation within populations suggests that the historical frequency and extent of seed dispersal by overland flooding has strongly affected the genetic structure of populations. Despite founder effects and population bottlenecks, small and large populations had similar levels of genetic variation. We found no evidence of hybridization. All extant populations of C. palmatum are genetically variable and distinct. We recommend that hydrologic connectivity be considered if seeds are collected and sowed with the intent of increasing the size of natural populations or creating experimental populations.