Cirsium hydrophilum is an endemic plant species of the San Francisco Bay Area in California composed of two geographically and edaphically separated varieties. Cirsium hydrophilum var. hydrophilum is adapted to brackish tidal wetlands in the San Francisco Bay Estuary and, C. hydrophilum var. vaysei to mountainous serpentine freshwater wetlands. Both varieties are recognized as federally endangered because of their small population sizes. In fact, C. hydrophilum var. hydrophilum was presumed extinct for several decades before its rediscovery. A population genetics project analyzed SNP data recovered from GBS sequencing to assess the genetic diversity of these critically endangered taxa. We confirm that the varieties are closely related but from distinct genetic clusters suggesting that there is no active gene flow among the two varieties. Across the known distribution of C. hydrophilum var. hydrophilum, four total genetic clusters were recovered that correlate with geographic localities of Hill Slough, Peytonia Slough, First Mallard Branch and Second Mallard Branch of Suisun Slough. Statistical analyses indicate despite a finding that C. hydrophilum var. hydrophilum is highly inbred, gene flow was detected among the four genetic clusters (i.e., populations). A similar pattern was uncovered for C. hydrophilum var. vaseyi. Given these insights we make recommendations for conservation managers involved in habitat restoration in areas where these taxa are endemic and sites are already identified for restoration.