Isozyme, randomly amplified polymorphic DNA, and ribosomal DNA analyses were used to evaluate the genetic distinctness and diversity of the endangered island endemic Malacothamnus fasciculatus var. nesioticus (Santa Cruz Island bush mallow). Analysis of amplified DNA profiles and electrophoretic data indicates that var. nesioticus is genetically distinct from other varieties within the species. No isozyme or amplified DNA variation was detected among individuals of nesioticus populations, but restriction site analysis of ribosomal DNA revealed the presence of three closely related genotypes within one of the nesioticus populations. Apparent clonal structuring was found in both nesioticus populations and in one mainland population, var. nuttallli. Results from these analyses provide the background necessary for the design of conservation efforts with recovery goals that insure the long‐term survival of Malacothamnus fasciculatus var. nesioticus.