SUMMARYPolymorphic nuclear microsatellite loci were used to characterize genetic variation in contemporary and historic populations of the San Clemente Island loggerhead shrike (Lanius ludo icianus mearnsi), an endangered bird with a current population of about 30 individuals, that is endemic to one of the California Channel Islands. We also compared the population of the shrike with two contemporary populations of the still abundant subspecies, L. l. gambeli, which live 120 km away on the adjacent mainland. The current population of L. l. mearnsi has 60 % of the genetic variation of the mainland shrike populations and is strongly differentiated from them. Comparison of living birds with 19 birds collected in 1915 shows that most of the variation within the island population was lost before the recent 90 % decline in population size, and the 20 % decrease in variation this century is probably attributable to genetic drift. Mitochondrial DNA control region sequence data from 80-year-old specimens show that there may have been limited introgression to L. l. mearnsi, this century, from another island subspecies, L. l. anthon i, found in the northern Channel Islands. Today, gene flow between L. l. mearnsi and mainland L. l. gambeli is very low, even though a few mainland birds visit the island annually. The island subspecies population has evolved sufficient genetic independence to justify ongoing conservation efforts to counter demographic collapse and genetic erosion ; the course of genetic erosion can now be monitored noninvasively, as demonstrated by this study, based on DNA amplified from feathers.