Varroadestructor is an invasive alien species that has been reported parasitizing the endemic honey bee of Madagascar, Apis mellifera unicolor, since 2010. Studying its nuclear genetic diversity and structure was our main goal. Using 11 microsatellite loci and 344 mites collected from 12 apiaries, we observed a low genetic diversity, with only 8 multilocus genotypes (MLG) identified. V. destructor populations form a single genetic cluster, clonal richness ranged from 0.02 to 0.20, and number of MLG within apiaries varied between one and six MLGs. About 69.5% of the mites analyzed harbored the same genotype (100%, homozygous), and 23.3% had a genotype differing by a single allele. The overall low diversity observed suggests one or multiple introductions of similar genotypes. The greater abundance of MLGs in High Land apiaries (eight MLGs) than on the east coast (two MLGs) and the presence of particular MLGs in High Land apiaries favor the hypothesis that V. destructor has been first introduced close to the international airport, and then spread to other regions by commercial exchanges.