A study of 35 colonies of Cordyfanlhus marilimus subsp. palustris in salt marshes of Tomales Bay, California, revealed habitat relationships, including patterns of co-occurrence and cover values of associated species, and examined the possible effects of spatial distribution on the occasional failure of annual colonies to appear. The presence of hemiparasitic C. m. subsp. palustris was strongly associated with the presence of Triglochin concinna and Limonium californicum. Covariance of cover values within a large colony of C. m. subsp. palustris corroborated the survey results for T. concinna, but was inconclusive for L. californicum. Increased species richness and decreased vegetation height were also valuable predictors of greater C. m. subsp. palustris cover. A three-year investigation of biogeographic relationships suggested that annual probability of a colony to appear was influenced predominantly by patch size and C. m. subsp. palustris density rather than by sizes or distances of other nearby colonies or populations. We speculate that this reflects very low probabilities of seed dispersal among C. m. subsp. palustris colonies.