In this study we aimed to develop a sequence-specific multiply-primed RCA for selective plasmid amplification from sponge samples and further characterize the sponge plasmidome via Illumina next-generation sequencing. Plasmid DNA obtained from sponge (Cinachyrella sp.) microbial communities and a bacterial symbiont (Vibrio sp. CyArs1) isolated from the same sponge species (carrying unknown plasmid) were used to develop and validate our methodology for selective RCA.