We investigated population dynamics, genetic diversity and spatial structure in the aphid species Macrosiphoniella tanacetaria, a specialist herbivore feeding on tansy, Tanacetum vulgare. Tansy plants (genets) consist of many shoots (ramets), and genets are grouped in sites. Thus, aphids feeding on tansy can cluster at the level of ramets, genets and sites. We studied aphid population dynamics in 1997 and 2001 and found that within sites: (i) at any time, aphids used only a fraction of the available ramets and genets; (ii) at the level of ramets, most aphid colonies survived only one week; (iii) at the level of genets, mean survival time was less than 4 weeks; and (iv) colonization and extinction events occurred throughout the season. We sampled aphids in seven sites in the Alsace region, France (4–45 km apart) and two sites in Germany in 1999 to study genetic structure within and between populations. Genetic analyses using nine microsatellite loci showed that: (i) genotypic variability was high, (ii) none of the populations was in Hardy–Weinberg equilibrium, (iii) heterozygote deficits and linkage disequilibria were frequent, and (iv) all populations were genetically differentiated, even at a small geographical scale. Renewed sampling of the Alsace sites in 2001 showed that three populations had become extinct and significant genetic changes had occurred in the remaining four populations. The frequencies of extinction and colonization events at several spatial scales suggest a hierarchical metapopulation structure for M. tanacetaria. Frequent population turnover and drift are likely causes for the genetic differentiation of M. tanacetaria populations.