Host genotype may shape host-associated bacterial communities (commonly referred to as microbiomes). We sought to determine (a) whether bacterial communities vary among host genotypes in the water fleaDaphnia galeataand (b) if this difference is driven by the genetic distance between host genotypes, by usingD. galeatagenotypes hatched from sediments of different time periods. We used 16S amplicon sequencing to profile the gut and body bacterial communities of eightD. galeatagenotypes hatched from resting eggs; these were isolated from two distinct sediment layers (dating to 1989 and 2009) of a single sediment core of the lake Greifensee, and maintained in a common garden in laboratory cultures for 5 years. In general, bacterial community composition varied in both theDaphniaguts and bodies; but not between genotypes from different sediment layers. Specifically, genetic distances between host genotypes did not correlate with beta diversity of bacterial communities inDaphniaguts and bodies. Our results indicate thatDaphniabacterial community structure is to some extent determined by a host genetic component, but that genetic distances between hosts do not correlate with diverging bacterial communities.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00248-022-02011-x.