Barnacles are conspicuous members of rocky intertidal communities and settlement of the final larval stage, the cyprid, is influenced by the presence of biofilms. While modulation of cyprid settlement by biofilms has been studied extensively, the acquisition of a specific microbiome by the settling larva has not. This study investigated settlement in the field of Semibalanus balanoides in two consecutive years when the composition of the benthic bacterial community differed. In both years, settling cyprids adopted a specific sub-set of benthic bacteria that was distinct from the planktonic cyprid and the benthos. This microbiome was consistent, regardless of annual variability in the benthic community structure, and established within hours of settlement. The results imply that a natural process of selection occurs during the critical final transition of S. balanoides to the sessile form. The apparent consistency of this process between years suggests that optimal growth and survival of barnacles could depend upon a complex inter-kingdom relationship, as has been demonstrated in other animal systems.