Malva assurgentiflora (Kellogg) M.F. Ray [Lavatera assurgentiflora] (Malvaceae) is a shrub endemic to four of the eight California Channel Islands: San Miguel, Anacapa, San Clemente, and Santa Catalina. Earlier population genetics and morphological studies have supported the recent recognition of subsp. glabra on San Clemente and Santa Catalina Islands. Subspecies assurgentiflora of the northern Channel Islands is quite rare, originally documented on San Miguel and on two of the three islets of Anacapa Island. Both Middle and West Anacapa islets populations have been extirpated over the last two decades, although seed from Middle Anacapa Island has been used to generate plants that have been introduced on East Anacapa. San Miguel Island has two naturally occurring populations with fewer than 300 plants total. Here we use population genomic techniques to 1) assess if genomic data continues to support taxonomic circumscription of northern island plants as differing from southern island plants; 2) investigate the within-island and between island genomic diversity of remaining plants on San Miguel and Anacapa; 3) determine the genetic provenance of plants in horticultural settings on the mainland and across the archipelago; and 4) identify the highest value conservation seed banking targets. Our sampling includes 150 individuals from across the range of both currently recognized subspecies as well as horticultural settings. Our results are consistent with earlier microsatellite studies and show a clearly that populations of subsp. glabra on San Clemente and Santa Catalina samples are as genetically distinct from each other as from the northern Channel Island populations, and merit taxonomic recognition. Samples from presumed horticultural settings share ancestry with plants from Anacapa Island. Unexpectedly, results also identify plants from a presumed historic horticultural setting on Santa Rosa Island as genetically most similar to those on San Miguel Island. These results forced a careful reanalysis of the provenance of the Santa Rosa Island plants and potential focused conservation efforts to preserve these unique genotypes.