Summary Marine sponges host diverse communities of microorganisms that are often vertically transmitted from mother to oocyte or embryo. Horizontal transmission has often been proposed to co‐occur in marine sponges, but the mechanism is poorly understood. To assess the impact of the mode of transmission on the microbial assemblages of sponges, we analysed the microbiota in sympatric sponges that have previously been reported to acquire bacteria via either vertical ( C orticium candelabrum and C rambe crambe ) or horizontal transmission ( P etrosia ficiformis ). The comparative study was performed by polymerase chain reaction‐denaturing gradient gel electrophoresis and pyrosequencing of barcoded PCR ‐amplified 16S rRNA gene fragments. We found that P . ficiformis and C . candelabrum each harbour their own species‐specific bacteria, but they are similar to other high‐microbial‐abundance sponges, while the low‐microbial‐abundance sponge C . crambe hosts microbiota of a very different phylogenetic signature. In addition, nearly 50% of the reads obtained from P . ficiformis were most closely related to bacteria that were previously reported to be vertically transmitted in other sponges and comprised vertical–horizontal transmission phylogenetic clusters ( VHT clusters). Therefore, our results provide evidence for the hypothesis that similar sponge‐associated bacteria can be acquired via both vertical and horizontal transmission.