In addition to its high biodiversity, the California Floristic Province contains over 1600 rare taxa, including many endemics restricted to specific soil types and habitats. In the highly urbanized San Francisco Estuary, these narrow endemics face additional limitations from habitat destruction and modification, prompting an interest in their conservation and management. One such taxon, the Federally listed Cirsium hydrophilum (Greene) Jeps. var. hydrophilum (Suisun thistle), is restricted to two or three populations, and may face limitations beyond past habitat loss. In this study, we investigated life history limitations that may contribute to rarity in C. hydrophilum var. hydrophilum. We documented low seed set, high seed predation by beetle larvae, low localized wind dispersal of seeds, and possible inbreeding in smaller patches. Because seeds did not have a stringent germination requirement in the lab, however, restoration or introduction of new populations from seed is possible. Using seeds from larger source populations could increase success of reseeding, as could adding seeds to augment potentially low genetic diversity in existing smaller subpopulations. Further study is needed to understand the ecology of seed predators, the relative importance of seed set and seed germination in the field, and to confirm our potential finding of reduced genetic diversity and inbreeding. Though the causes and consequences of rarity may differ for each species, this study explores several research directions that could be productive for understanding other California endemic Cirsium and rare wetland endemics.